


Evangelion X Godzilla Part II: Sin From Genesis

by AlphaBeta17



Series: Evangelion X Godzilla [2]
Category: Godzilla - All Media Types, Neon Genesis Evangelion
Genre: Action/Adventure, Alternate Universe, Canon-Typical Violence, Character Reinterpretation, Crossover, Drama & Romance, F/M, Science Fiction
Language: English
Status: Completed
Published: 2020-03-10
Updated: 2020-05-29
Packaged: 2021-03-01 00:40:54
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings, Graphic Depictions Of Violence
Chapters: 13
Words: 34,906
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/23486221
Author URL: https://archiveofourown.org/users/AlphaBeta17/pseuds/AlphaBeta17
Summary: Following the events of Evangelion X Godzilla: A God Incarnate, Shinji must face the horrifying reality of what happened to him and accept his role in protecting the world. Meanwhile, a destructive force is about to reach Earth, intent on wiping out all life. Alongside Rei and Asuka, Shinji must fight to protect everyone he cares about, or face annihilation.
Relationships: Ayanami Rei/Ikari Shinji
Series: Evangelion X Godzilla [2]
Series URL: https://archiveofourown.org/series/1708768
Kudos: 1





	1. Ghidorah

**October 9th, 2000 (Planet X)**

Ghidorah roared with each of his three heads as he released a shockwave of gravitational energy towards the ground miles below. Nearby airships that hadn't already been destroyed in the battle were knocked out of the sky and sent plummeting.

Across the entire planet, citizens desperately tried to seek shelter as the atmosphere continued to break down and the continents began to fold. The strike against the 150 meter tall Ghidorah had failed, leaving the extra-terrestrial monster free to wreak havoc. Its sole goal was the destruction of Planet X.

* * *

Planet X. A once thriving world in the Andromeda Galaxy that had been doomed ever since its brightest minds had tampered with one of Ghidorah's organic beacons twenty years before. The resulting explosion near the planet's equator had killed billions and sent the world into an apocalyptic state.

The resilient Xilien race had refused to give up, however. They'd clung to life with a tenacity that surprised Ghidorah. Most planets that triggered one of his beacons were totally unprepared for his arrival, but this one had been ready with multiple monsters, mechs, and a vast armada of airships.

It had taken him a little longer than usual, but he had easily destroyed them all. He was the most powerful being in the universe after all. Created by an intergalactic civilization millions of years ago, he had been meant to be the ultimate weapon in their war against another, stronger intergalactic civilization.

He had done exactly what his creators had wanted. He had systematically wiped out the enemy, driving them to extinction over the course of several generations. By the time his task was completed, the ones who had made him were long dead, their grandchildren now the ones in control of him.

He had wondered what he would do after eighty years of galactic conquest, but he would never have expected to be brushed aside and sent 'into retirement' with his usefulness at an apparent end.

In his rage, he had broken free of their control and destroyed them. They had fought hard against him and even created two monsters to fight him. Based off of his original design, his creators had named them Desghidorah and Keizer Ghidorah respectively. While they both possessed the same massive wings, three heads, regenerative powers, and the ability to manipulate energy that Ghidorah had, they were made to be bulkier and given an additional pair of legs.

Ghidorah had killed them both, of course, earning himself the nickname of 'King' Ghidorah from the frightened lower classes. Many tried worshipping him, hoping that their collective adoration would sway him.

It hadn't.

Once they were all destroyed, Ghidorah had set out in search of more civilizations to destroy. It was the only really interesting thing that broke up his monotonous existence.

After aimlessly wandering for over a million years, randomly happening upon inhabited planets, Ghidorah had grown bored. Most planets lacked intelligent life that could fight back. They just weren't fun to destroy. In his boredom, he had begun experimenting with self-evolution, a feature his creators had added but never used, deeming it 'gimmicky'. It took thousands of years to take effect, but he had the time and patience to create for himself the perfect tool.

He had developed the ability to produce organic beacons that he could lay as eggs and fire off into the universe. They would be attracted by lifeforms, and crash-land on planets. They would lay dormant until they were disturbed by intelligent life, after which they would explode, releasing so much energy that he could detect it from wherever he was in the near universe.

It had taken some time, but now they worked like a charm. He had destroyed thousands of civilizations in the past million years alone.

Now all he had to do was finish off Planet X and move onto the next one.

* * *

Suddenly, Ghidorah sensed something rocketing towards him, coming from thousands of miles away, on the other side of the planet. He stopped his planetary destruction to take notice of it and was pleasantly surprised to discover that it seemed to be one more monster. Fighting other monsters was always the most fun part of destroying worlds since every intelligent civilization inevitably brought about the rise of monsters.

After several minutes of patiently treading air with his massive golden wings, the monster appeared over the curve of the Earth. Ghidorah narrowed his three pairs of eyes.

The monster was bizarre. A 100 meter tall bipedal monster with large red fins jutting out of its back, its face had a beak, horns, and a red visor covering its eyes. Jutting out of its chest was a row of whirring spikes, and instead of hands, its arms ended in large metal hooks, with smaller ones in place of its feet.

Yes, it was one of the strangest monsters Ghidorah had ever come across.

The people of Planet X called it Gigan. A cyborg monster developed by terrorists, the impending doom of the planet had forced them to hand the cyborg over to the planet's military in hopes of saving the world. Now it was the only thing standing in Ghidorah's way.

Gigan released a high-pitched roar as it flew directly towards Ghidorah. A red laser beam fired from its visor and Ghidorah swerved in midair to avoid it. He roared in anger and launched himself at Gigan, legs outstretched, ready to grapple the smaller monster.

Ghidorah's legs clamped down on Gigan's arms and held them to the side while he used his heads to attack Gigan, biting at its face. To Ghidorah's surprise, Gigan thrust itself against his chest, using its spinning chest blade to lacerate Ghidorah's usually impenetrable golden scales.

Ghidorah roared in pain and dropped Gigan, using his wings to retreat from the bladed monster. Gigan levitated in midair for a moment before continuing after Ghidorah, swinging its metal hooks back and forth, trying to slash at the dragon. Ghidorah flew in a wide circle, trying to outmaneuver the smaller and more agile Gigan. He opened his right and left head's mouths and launched electrical beams at Gigan, who blocked them with its metal hooks, which absorbed the electricity.

Gigan fired its eye beam at Ghidorah again, who spun in midair to avoid the explosive laser. He angled himself towards the ground miles below and began to dive, trying to lure Gigan into following him.

Gigan took the bait, plunging after Ghidorah. It launched another beam at Ghidorah, who allowed himself to bee hit, a large explosion engulfing his body from where the laser struck him. He suddenly extended his wings, halting his descent. He raised his heads upward, ready to clamp down onto Gigan, who was only seconds behind him when the cyborg released a strange squawking noise and suddenly vanished in a spray of red sparks. Ghidorah swung his heads around side to side in confusion, only for one of his wings to be suddenly sliced off at its base by Gigan's hooks.

Gigan had teleported underneath Ghidorah, a relatively new technological advance for the people of Planet X. It could only work at short ranges, and Gigan had used it to its full potential in combat, having swung its left arm in a wide arc while spinning past Ghidorah.

Ghidorah roared in pain and began to plummet towards the ground in freefall while Gigan continued smoothly with its spin into a dive, rocketing towards Ghidorah. Gigan lashed out and stabbed Ghidorah in the chest with both of its hooks, its human controllers hoping to fatally wound the dragon.

This was their big mistake.

Ghidorah's right and left heads reached out and grabbed hold of Gigan once again, but this time, the dragon began injecting Gigan with electricity, overheating its mechanical components, while his center head clamped down onto Gigan's head. Gigan couldn't free itself from Ghidorah, and so they began to freefall together while Ghidorah used his sheer size to wrestle with Gigan, angling Gigan beneath himself.

Gigan tried desperately to scramble free, even attempting to teleport out of Ghidorah's grasp, but each teleport attempt would only bring the monster with him. Ghidorah roared in triumph as they slammed into the ground, Gigan taking the brunt of the impact.

Ghidorah slowly stood up and spread his wings, the one that had been sliced off already regenerating, while he pulled himself off of Gigan, the metal hooks sliding right out, leaving gaping wounds that began to regenerate after a moment. Ghidorah roared with each of his heads when he was fully healed, with not a scratch on his body, and reached down to finish off Gigan.

Holding the monster down with his right and left heads, he clamped down onto Gigan's neck with his center head and released a bolt of his devastating gravity beam, which tore the cyborg's head off, sending it flying into the air. Ghidorah then stuck his head down Gigan's exposed throat, using his long neck to plunge deep into its half-organic half-mechanical body. With his head deep inside Gigan, he began to charge up his gravity beam.

After several moments, he released a blast that caused Gigan's already lifeless body to be blown outward, sending bits of flesh and metal hurtling across the landscape, propelled by the force of the explosion of raw gravity.

Ghidorah was covered in blood and guts from the explosion, and used the electrical beams from his right and left heads to clean himself off, the electricity conducting through his golden scales, propelling the pieces of Gigan away with a crackle.

Ghidorah then returned to his task, satisfied with his appearance. He was a god, after all. He believed that he should look appropriately regal while ending the world for these pathetic Xilien beings.

Using his center head's gravity beam, coupled with massive flaps of his wings that spread raw power through the air, Ghidorah tore the planet apart. Billions died in a matter of hours while he used his powers to rip a hole open in the crust of the planet, allowing the planet's interior to cook the atmosphere away. The planet began to disintegrate around Ghidorah, who used his gravity beam to its full extent, sending it surging down into the planet's metallic core, where it was conducted and sent surging out in all directions, blasting the planet apart from the inside.

Ghidorah roared in triumph as he flew back out into space, leaving the shattered remains of Planet X behind him. He had done this thousands of times, but it never got boring, or unrewarding, to look back on what he, one singular being, could accomplish.

After several weeks of resting on a nearby asteroid, he took flight. As he began to pick up speed, aiming to leave the solar system of the Xiliens behind, he felt a sudden surge of energy. One of his beacons had just been triggered nearby. In fact, it was in the nearest major galaxy to the Andromeda Galaxy: the Milky Way Galaxy.

It would only take Ghidorah about 15 years to reach the galaxy, and then perhaps another couple of months to reach the particular solar system that contained intelligent life. Then, he would destroy that planet, along with its civilization. Nothing could stop him. There was nothing in the universe that could naturally evolve that could beat him.

He was a god. A being of infinite power.

He was King Ghidorah.

**Notes for the Chapter:**

> Welcome! We've finally made it to the second installment of Evangelion X Godzilla, and I couldn't be more excited! The entire story is planned out, and I can't wait to see how people react to some of the things I've got planned. Once again, there will be twelve chapters, released weekly on Tuesday nights.
> 
> I decided while outlining this entire story that I should begin with a chapter introducing Ghidorah, as he will (obviously) be the main villain of the story, and after teasing his existence in A God Incarnate, I figured I shouldn't delay his first real appearance.
> 
> All comments are welcome, I really enjoy hearing what you guys think!
> 
> Until next time!
> 
> -AlphaBeta17 (3/10/20)


	2. Awakening

**December 9th, 2015**

Rei walked down the sidewalk on her way to school. She passed several deserted office buildings before reaching where she usually crossed the street. She glanced both ways before starting across. Cars didn't come too often anymore, but it didn't hurt to check. Shinji had helped her learn to be more aware of her surroundings.

_Shinji._

It had been two months since Shinji's Eva had merged with Godzilla, and the young boy was still trapped inside his Entry Plug, which was buried somewhere inside the mass of flesh and metal that was both Godzilla and Eva-01. Rei ignored any thoughts of Shinji. He was still technically alive, but in a state of perpetual hibernation, along with both the Eva and Godzilla.

Following the disaster that was Godzilla's second attack on Tokyo-3, the UN finally stepped in. Command of Nerv had been stripped from Gendo and handed over to Misato, while Makoto had been promoted to Ritsuko's position. Before they could be questioned, however, Gendo, Ritsuko, and Ryoji had all vanished. Gone into hiding most likely. Ever since then, Misato and Makoto had been trying to figure out everything that they had done, but were nowhere closer to answers then they had been two months ago.

Drops of rain started to fall from the sky. Rei hurried her pace, not wanting to be caught in the torrential downpours brought on by year-round tropical storms in the post-Second Impact climate.

_One of the downsides to being more self-aware. I notice when I am physically uncomfortable now. Before I would not have minded getting caught in the rain. Now I do._

Left to rot, the entire central part of Tokyo-3 in a two-mile radius had been shut down and restricted. Containing most of the damage from the battle with Godzilla, those who remained in Tokyo-3 lived in the outskirts of the city now. Mostly they worked for either for Nerv or had been given exorbitant monetary incentives to stay behind to support the workers of Nerv. Or they were too poor to move. Rei had spent much of her time sitting in her apartment with Mari, who had become much less expressive in Shinji's absence.

_It is so quiet._

Even Asuka had been relatively subdued for the past two months. The shock and horror of what had happened to Shinji had driven much of the hunger from the ferocious girl away. Eva piloting wasn't as fun without someone with whom she could regularly claim to be better than. She would only ever show her growing internal fury during the Eva simulations, where her rage would result in unsteady, bloody battles.

Makoto had appeared quite lonely the past couple of months, what with his friends Maya and Shigeru being long gone. Rei had no clue why the nerdy technician had chosen to continue working for Nerv, but he was still reporting for work every day, working under Misato to run simulation tests for Asuka and Rei, alongside two new technicians that had taken Maya and Shigeru's places.

Both Rei and Asuka's Evas were fully repaired due to activating Orga's regenerative DNA, which Ritsuko had incorporated into all three Evas. Despite leaving no apparent records of how this new ability functioned, with the help of the new staff members, the ability was now able to be somewhat controlled manually.

Despite there being no monster attacks for the past two months, Misato insisted that Rei and Asuka still train, just in case another monster attacked.

_She will not say the real reason. We all know what it is._

_We train in case Godzilla wakes up._

_For the eventuality that Godzilla will wake up._

_Or worse, that what Ritsuko and Gendo claimed is true._

Rei shivered at the thought of Gendo. How he had leered at her for years, telling her that she was 'replaceable' and 'worth nothing.' How Misato had told her that Gendo claimed that Shinji's mother's consciousness was still inside Eva-01, and now Godzilla, to this day.

It was a terrifying prospect for Rei. If Shinji's father was Gendo, what could his mother be like? And worse, did that mean that every Eva had a soul inside of it that allowed it to function?

_Could there actually be someone inside my Eva? It sometimes felt like there was a malicious presence sharing my mind whenever I piloted the Eva. I could not recognize it at the time, but looking back, it is certainly a possibility._

Finally, there was the talk of an 'extraterrestrial being' that Gendo believed was coming for Earth. There was no possible scenario in which his crazy theory could be correct. Or at least that was what Rei would tell herself.

_If it is true, then please wake up Shinji. The world will need you more than ever._

As Rei reached the school and hurried inside, shaking drops of water from her hair, she allowed herself a brief moment to feel again.

_Please wake up Shinji. I need you._

* * *

Makoto yawned as he made his way onto the bridge of Central Dogma. Misato shot him a withering stare and he quickly straightened his posture before walking to his seat.

_She's been extraordinarily tense ever since the battle with Godzilla. One would almost think she had lost her own child in the battle. Well, in a way, she kind of did._

Makoto sat down and booted up his computers. Systems came online indicating that both Rei and Asuka's Evas were functioning normally.

_At least now I actually understand what most of these readings physically mean._

With Ritsuko gone, it had fallen to Makoto to take over as head technician for the Evas. With no clear way to gather information, he had been forced to figure it out by trial-and-error. Eventually, it had become too much, and after clearing it with Misato, he had brought on two new crew members for Central Dogma.

Miki Saegusa. An ecological neurologist. Cheery and studious, she had been working to re-establish contact with Shinji inside of Godzilla, possibly with supersonic frequencies. Her theory was that Gendo had been attracting monsters to Tokyo-3 with the use of a bioacoustic device, and she was working on a prototype capable of communicating with monsters. She was constantly claiming that 'Godzilla isn't a monster, in fact, he's innocent!'

Daisuke Serizawa. Expert in biomechanics. Cynical and serious, he had been examining the inner workings of the Evas in an attempt to understand more about how they functioned. He was at the center of trying to figure out the puzzle that was the fusion of Godzilla and Eva-01. As for the mental aspects of the incident however….

_Miki's our only hope for figuring that out without having access to Terminal Dogma._

Terminal Dogma sat beneath Nerv and was home to Ritsuko's many experimental chambers. While Misato had tried to get down there as soon as she had command of Nerv, Ritsuko had managed to install multiple security codes and firewalls making it nearly impossible for anyone else to access it. It was clear that she didn't want anyone knowing what sort of things she was hiding down there.

Misato had tried petitioning the UN to override the security measures to allow access, but the UN had stated in response that the best course of action was to 'forget about the crimes of the past and move on.' Misato had been furious, but there was nothing she could do. She directly reported to the UN now, and if she wanted to keep command of Nerv, she had to fall in line.

"Morning Makoto!" Miki waved cheerily at Makoto as she walked in. "Morning Miki," Makoto responded, shaking himself out of his thoughts. "Any luck?"

Miki sighed. "Nope. I tried scanning from the edge of the restricted zone, but I still wasn't able to pick up any readings to prove my theory. I'm not giving up though. I _know_ that Godzilla is warm-blooded! He has to be!"

Daisuke rolled his eyes as he entered. "It's unscientific to refer to Godzilla as a male. We have no idea if it even has a gender, and it'll just get you more attached to it, which is absurd anyway. Our role as scientists is to be as unbiased as possible, how many times have I reminded you of that?"

Miki narrowed her eyes at the stiff scientist. "Just about every single day since we started working here. It would do you good to lighten up a bit Daisuke!"

"I told you, call me Dr. Serizawa! I spent years achieving that title and you refuse to give me the proper respect!"

Miki scoffed. "I'm a doctor as well, but you don't see me demanding Misato call me Dr. Saegusa!"

Makoto chuckled. "She'd probably rip your head off if you did."

"That's enough everyone, let's get to work!" Misato's firm voice silenced the bickering scientists, who quickly took to their seats, not about to invite the wrath of Misato.

_I still can't believe I didn't leave with Maya and Shigeru. Now all I do is listen to Miki and Daisuke bicker all day, while Misato occasionally yells at them to be quiet. She was a lot more enjoyable to be around before all that stuff happened. Before she became so...angry._

* * *

Asuka lashed out at Godzilla with her twin Prog Knives drawn, slashing across the reptilian monster's stomach, spilling blood all over her Eva. She yelled as she plunged her fist into the bloody flesh, reaching for Godzilla's internal organs.

"Asuka. That is a waste of time," Rei quietly reminded the fiery girl.

"Shut up! I won't lose again!" Asuka screamed as she blindly tore into the monster.

Rei shook her head and backed up. She knew what was coming.

Godzilla's flesh began to regenerate, trapping Asuka's Eva's hand inside its torso. Godzilla stared down at the Eva with a ferocious look in its eyes before releasing a blast of its purple beam, which had by now been termed 'atomic breath' by Miki. The Eva was struck directly and blew up upon impact.

SIMULATION FAILED

SIMULATION FAILED

"Damn it! Somebody shut that stupid alarm off!" Asuka yelled in anger as Misato watched disapprovingly. "Why the hell won't anything work?! These sims are rigged! It's utter bullshit!"

Rei quietly exited her simulation Entry Plug and went to go shower while Asuka stumbled out of her own, still dripping in smelly LCL. She found Misato waiting for her. "Don't. I don't want to hear it," Asuka groaned.

"You know I have to. This is the seventh simulated battle with Godzilla alone that you've managed to get yourself killed, not to mention all the ones with other monsters. Do you honestly have a death wish? Or are you just plain stupid?"

"Of course not! I'm not stupid! How could you even say that?!" Asuka's voice began to rise in volume as she tried to stare down Misato, who's hard gaze was piercing through Asuka's arrogant mask. "I'm the best Eva pilot there is!"

"Even in simulations against monsters other than Godzilla, you have repeatedly failed again and again. Not due to lack of proficiency in piloting skills, of course. In terms of controlling yourself and thinking before charging in, you seem to have no intention of ever doing that, despite being told to do just that several times! You're insubordination and refusal to take orders is forcing my hand! Get your act together, or you're out of the Evangelion program!"

Asuka balled her fists. "You can't do that! No one else can pilot Eva-02 besides me! That would be billions of dollars wasted!"

"I am well aware of the situation. But I'd rather it go to waste than causing even more damage to Tokyo-3, and possibly your death. Get out of my sight. This conversation is done."

Misato turned on her heel and stalked off, while Asuka sputtered in anger. Years of always getting what she wanted in Germany had come to a bitter end following the battle with Godzilla, and she wasn't taking it well.

"Oh, bullshit! You're just mad that you got stuck with me alive instead of that stupid Shinji! If you would just accept that he's dead already-"

Misato whirled around and strode towards Asuka, grabbing her by the throat. Misato's eyes blazed with untold fury as she roared into Asuka's face.

"SHUT UP! SHUT UP BEFORE I KILL YOU! YOU HEAR ME?!"

Misato threw Asuka against the wall and stared down at her. Blood pounded in her ears as she turned and ran, fury coursing through her veins as she tried to shove down rising feelings associated with Shinji in her mind.

Foremost being guilt.

* * *

On the outskirts of Tokyo-3, a patch of vines began to constrict and grow. Reacting with numerous chemicals that had been applied to them the previous night, a large shape began to form. The vines came together to create an independent living being made exclusively of vegetation. A large maw began to come into being filled with rows of serrated teeth while eyes sprouted and began to flit about. A monster was coming into being in a matter of minutes.

Back at Nerv, it was immediately picked up on the scanners.

"Um, is anyone else seeing this, or does there seem to be a giant plant monster rising up out of nowhere?" Miki's voice warned. Daisuke immediately verified the findings and swung on Makoto. "Sound the alarm, monster attack incoming!"

* * *

Rei pulled her new weapon, the Progressive Katana, from its large sheath on the Eva's waist. She swung it around in a wide arc before settling into a defensive stance. Nearby, Asuka already had her newly created twin Prog Knives drawn. They had both been practicing with these weapons in the simulations, but this would be the first time they would be used in battle.

It would also be the first battle since Godzilla.

"Rei, Asuka. This monster has been named Biollante. Its physical specs are as follows. 120 meters tall with limited movement, but massive power. Composed entirely of plant matter, the test bombings on it proved that it has regenerative powers. Approach with caution, as it probably has powers we can't yet detect. Remember, while we do have control of the Eva's regenerative powers now, manual activation of these powers take time, so if you get disabled out there, you're done for. Good luck."

Makoto couldn't help but raise his eyebrows at Misato's curt analysis. Miki and Daisuke were both nervous about the battle. They'd seen the footage from the previous battles, and knew that just about anything could happen. Miki was unusually focused, while Daisuke had a deadly serious expression on his face. Makoto hoped that along with Misato, they could help claim victory.

Nobody wanted a repeat of the battle with Godzilla.

"Rei, Asuka. Charge!"

* * *

WAKE UP

WAKE UP

_What? Who's saying that?_

IT'S ME

THE EVANGELION

_Wait what? What happened?_

IN ORDER TO SURVIVE

I MERGED US WITH GODZILLA

_You did what?_

I JUST DETECTED A NEW MONSTER

IT'S ON THE OUTSKIRTS OF YOUR PUNY CITY

WOULD YOU LIKE TO ENGAGE IT

_Wait, you're saying there's a new monster? How long have we been stuck in here?_

WOULD YOU LIKE TO ENGAGE THE MONSTER

_This doesn't make any sense. We merged with Godzilla?_

YES

I AM NOW GODZILLA AND THE EVANGELION

_That makes no sense!_

IT DOES NOT HAVE TO

I ASK ONE FINAL TIME

WOULD YOU LIKE TO ENGAGE THE MONSTER

_If I do, can I get out of…..whatever this is?_

YES

_Then yes. Let's fight this monster._

**Notes for the Chapter:**

> Well, the real world certainly went crazy in the past week! Hopefully, this doesn't all end in the Third Impact lol.
> 
> Until next time!
> 
> -AlphaBeta17 (3/17/20)


	3. Biollante

**December 9th, 2015**

Rei circled her Eva around behind Biollante while Asuka came at it from the front, hoping to disorient it by attacking at the same time as Rei.

Asuka's Eva dove at Biollante with both of her Prog Knives outstretched. Vines flew up to attack her, and she sliced them away in midair. Landing right next to Biollante, Asuka began stabbing at the plant monster, dueling with its many vines, which were flailing about, trying to grab her Eva. No matter how many vines she cut, there always seemed to be more.

Behind Biollante, Rei held her Prog Katana in a defensive pose, ready to strike.

"Now!" Misato yelled.

Rei lunged forward and drove her katana straight into the center of Biollante's mass, piercing right through the layers of plant matter. Green acidic pulp squirted out all over her Eva, causing her to grit her teeth in pain, and Biollante bellowed in pain. It was an eerie, almost tragic cry.

Biollante swung its massive head around to peer down at Rei's Eva. It lashed at her with its mouth, trying to grab her Eva in a death grip, which Rei was barely able to avoid by pulling her katana free and jumping backward.

Makoto turned to Misato."It appears that while our Progressive weapons are effective against Biollante, its sheer size means that they don't do enough damage to cripple it!"

"What should we do?!" Asuka yelled as her Eva backflipped in the air to avoid being grabbed around the legs by stray vines.

"Asuka, try hitting at critical points like the back of its head. If our weapons can pierce it, then we might be able to land a critical blow there," Misato commanded.

With Biollante still distracted by Rei, Asuka jumped her Eva up onto Biollante and drove her knives into the back of its neck, unleashing a flood of green pulp that blasted her Eva off and back down to the ground below.

Miki suddenly gasped. "Rei, behind you!"

Mouthed vines broke out of the broke behind Rei, baring teeth that resembled how a venus fly trap would look. The vines lunged at Rei's Eva, biting down onto its limbs. Rei flailed in her cockpit, trying to free herself, while Asuka got her Eva to its feet and tried attacking again, this time by keeping in constant motion, running circles around the large monster while it tried to grab her, to no avail.

Biollante grew frustrated with the battle. The Evas were both considerably smaller than she was, and while she would easily overwhelm either one on one, having to fight both at the same time meant her attention was divided. Biollante roared in annoyance, its high pitched screech echoing through Tokyo-3.

Makoto noticed a jump in radiation on his monitors. "Misato, I think Biollante's about to unleash a new attack!"

Biollante managed to connect one of her Eva's vines with Asuka's Eva, sending it crashing to the ground. Before anyone could react, large amounts of acidic sap began to spit out of her maw, sizzling upon contact with Asuka's Eva, a large glob landing on its head, burning into its eyes. Asuka screamed at the sudden torturous sensation and scrambled forward, blindly swinging her knives.

"Asuka, no!" Misato yelled.

But it was too late. Biollante grabbed Asuka's Eva in her massive crocodilian mouth, snapping its metal plating with loud cracks before throwing it across the city with a swing of her massive head.

With Asuka out of the way, Biollante turned her attention to Rei, who was still trying to escape the grips of her mouthed vines, which were beginning to twist and contort the Eva's limbs in different directions, drawing cries of pain from the girl.

Biollante picked the Eva up and began to pull its limbs in different directions, trying to pull it apart, while Rei screamed in pain. It felt like her limbs were being pulled out of their sockets, and Asuka wasn't doing any better, with her Eva lying crippled and blinded.

Makoto slammed her fist into a nearby wall. "Damn it!"

Right as Rei closed her eyes to brace herself for the sensation of her limbs being torn off, a haunting roar pierced through the air, startling Biollante, which dropped Rei's Eva to the ground. Rei scrambled her Eva away, limping from the pain of the Eva's joints being stretched to their limits, while Biollante turned her head to face the source of roar, which came from the decimated restricted center of Tokyo-3.

Misato gasped at the sight on the monitors, while Miki, Daisuke, and Makoto froze in shock.

It was Godzilla. And it was moving for the first time in two months.

Fused with Eva Unit-01, the abomination released another roar. It was the same roar from before: a mix of Godzilla's roar, an Eva's bellow, and Shinji's scream.

Biollante narrowed its eyes at the new, strange rival, which started to walk forward carefully, testing each step like it was about to fall over. She had noticed it as soon as she had been formed, but had ignored it, recognizing it as in a state of hibernation. Now, it appeared to be fully awake, and ready to battle.

Overcome with emotions, Misato could only say one thing.

"Shinji…..you came back….."

* * *

Inside of his Entry Plug, swimming in two-month-old LCL, Shinji Ikari gingerly moved the Eva- no, Godzilla, forward. There was a large plant-like monster in Tokyo-3, and it had been trying to tear the limbs off of what looked like Rei's Eva. A single massive roar had been enough to get its attention, and now, it was coming right for him, as fast as it could move by pulling itself forward with its vines.

_Good._

REMEMBER

WE WILL WORK TOGETHER

_Yes, I know._

Right as Biollante was about to grab Godzilla with its mouthed vines, Shinji suddenly threw Godzilla to the ground, dodging underneath the outstretched vines. Godzilla's dorsal plates, which were now serrated, sliced through Biollante's vines, spraying itself with Biollante's acidic pulp.

Shinji could feel the acid on his skin, just like he would have if he was piloting a normal Eva, but it failed to register as painful in his mind.

WE HAVE THE POWER OF GODZILLA

THIS THING CANNOT HURT US

Godzilla lashed out at Biollante, catching its jaws in a right hook that sent the giant plant monster sprawling. Back at Nerv, Makoto watched in shock. "The amount of force required to do that…..it's mind-boggling!"

Godzilla grabbed Biollante's lower jaw and yanked on it, pulling it off with a loud squelching noise. Biollante began convulsing while Godzilla jumped onto it and began using its now-humanoid arms to grip at and tear pieces of Biollante off in a vicious display of carnage.

Inside Godzilla, fueled by the ever-present rage of both the Eva and Godzilla, Shinji began to give in to the massive surge of rage and power.

_It tried to hurt Rei. I will kill it._

_I WILL KILL IT!_

In a flurry of motion that looked unnatural from something of its size, Godzilla began to pummel Biollante, each impact of its kicks and punches leaving a clear impact on the monster.

Miki watched the violence with her mouth agape while Makoto looked on in resignation, far too used to the brutal violence. Daisuke seemed entranced, and Misato was watching with an expression that had been long since absent from her face.

Hope.

With a sudden burst of energy, Godzilla began to glow bright green, its dorsal plates lighting up from the tip of its tail to its Eva-armored head.

Misato knew what was coming before it happened. "Oh my god….."

Godzilla opened its mouth and sent forth a blast of atomic breath, now green in color, which pierced into Biollante, overloading its nervous system from the sudden surge in nuclear power. With a high pitched screech of terror, Biollante burst apart, raining acid over Tokyo-3.

Shinji felt a surge of power flood his soul as he joined Evangelion Unit-01 in lifting Godzilla's head skyward, unleashing a roar of triumph that shook the city.

After lasting for several long moments, Godzilla slumped forward, all energy seemingly draining out of it. It began to shamble towards Nerv, collapsing to the ground in front of the giant steel pyramid. After a moment of silence, the armor plating covering the back of its neck parted, allowing Shinji's Entry Plug to partially eject.

Misato stared at the live footage for a moment before turning and sprinting out of Central Dogma. "Get me an ejection crew! We need to get Shinji out of there!"

* * *

**December 10th, 2015**

Gendo Ikari tipped his glass back and took another huge gulp of beer before slamming it down, empty. He was sitting in one of the few remaining bars in Tokyo-3. With most of the population that had stayed working for Nerv, few, if any, went out to drink.

"C'mon guys. Don't keep me waiting," he mumbled to himself.

After several minutes of sitting in impatient silence, Ritsuko Akagi and Ryoji Kaji finally joined him.

"Any word?"

"No. But it appears that Shinji was recovered alive. He's in a coma, but they think he'll wake up in the coming few days."

"Really."

"That's all I overheard. The mechanical crew don't know too much, only what they see with their own eyes."

"I see. But I take it that by all accounts, our little experiment went perfectly?"

"Yes. It got Yui to finally stop shielding Shinji. She finally woke up Godzilla from hibernation. I still have no clue why she thought that would be a good idea, but maybe you're wrong. Maybe she's not in control of the Evangelion."

"Of course she's in control. She is its soul. If she's not, then that means that the Eva itself has a personality. That's simply preposterous. It's a monster."

"Either way, the plan worked. A huge monster appeared, and Godzilla defeated it. Now, Shinji's out, and hopefully whoever is in control of Godzilla now will be able to prepare for what's coming."

"We have no clue what form it will take. It could be anything. A fleet of green men. A blob of goo. Whatever it is, it has to be intelligent, hyper-evolved, and malicious. If the world will survive, Godzilla has to defeat it. It's the only way."

"We can only hope Shinji won't have to be present inside of the Entry Plug in order for it to operate. If he has to, then he'll compromise the only chance we have at preventing the destruction of our planet. He'll doom us all."

* * *

Long after Ryoji left, and long after Ritsuko had later fallen asleep beside him back at his apartment, Gendo sat up and stared out the window at Tokyo-3. He used to be the most powerful person in the city, and now, he was relegated to living in hiding.

Someday, it would all be worth it. He had spent years planning. Even something unexpected like the fusion of Godzilla and Eva Unit-01 would not prevent his reunification with Yui.

He hadn't gone to so much trouble with Rei for no reason.

_I'm very fortunate that nobody working at Nerv right now ever met Yui. Otherwise, they'd recognize her face on Rei in a heartbeat._

* * *

**December 11th, 2015**

Rei stared down at Shinji. It felt unreal to see him again after him being, for all intents and purposes, dead. She had tried her hardest not to think of him the past two months. The one who had opened the door for her eyes to the world as it was.

She had stood in the doorway, but it was him that had taken her hand and helped her take the first step. Right as she had begun to walk, he had vanished, and she had been forced to walk alone.

Now, he was back.

Lying in his hospital bed, he was physically completely fine. The doctors said he would probably awaken in the coming days, but they weren't sure what his mental state would be like.

Rei didn't even begin to consider the possibility that he might have lasting damage. If she did, she would go crazy with anxiety.

_I have no control over what will happen in this case. Therefore, I will not spend time worrying about it. What happens will happen, and I will have to live with it._

Misato stepped into the room. "Oh. Rei. I see you've already found him."

"Yes. I will guard him until he awakens."

Misato sighed. "You don't have to do that Rei."

"Yes, I do. He would do the same for me."

Misato didn't know how to answer that. Rei wasn't wrong.

"Rei….."

"I know," Rei quietly interrupted. "I have a reasonable amount of intelligence."

Misato raised her eyebrows. If this wasn't Rei, she would probably have snapped at the seemingly sarcastic remark, but in Rei's case, she probably hadn't meant anything by it. She was stating a fact.

"OK. I just want you to be prepared in case….." Misato couldn't finish. The past two months of running Nerv had turned her into a hard leader who pushed emotions below the surface. A far cry from who she had been before.

"I know, Misato. Thank you," Rei responded.

Without another word, Misato turned and left the room, leaving Rei to her vigil.

* * *

**December 15th, 2015**

Rei was returning to her post after school like usual, only to find someone already sitting in her chair, watching Shinji. Rei instinctively flattened her gaze, years of conditioning not having vanished overnight.

"Asuka. Why are you here?"

Asuka turned and smirked at Rei. "What, jealous?"

"Why are you here? You do not care about Shinji."

Asuka rolled her eyes. "OK OK, blue-hair. I get it. I'm a bitch. That doesn't mean I'm not slightly concerned about whether or not he survives. Remember, he did save the day. Even _I_ can express gratitude. Or am I just too much of a cruel girl to grant a wimp like him that?"

Rei's expression hardened, her mask slipping off. "Go. You do not belong here."

"Oh really? Who are you to decide that? What, you think because you got the fancy new sword for the Eva, that makes you my superior? C'mon. You have the personality of sandpaper for crying out loud! Personally, I'm very curious about this whole 'mental damage' idea. Maybe he'll be totally different. He was stuck inside of a radioactive monster that fused with a horrifying creation of Nerv for two months. That's got to change something in a person."

"Dr. Serizawa says that Ritsuko designed the Entry Plugs to be able to safely protect a person from radioactivity."

"He didn't design the damn things though, did he? It's OK. I'm sure your boyfriend will be perfectly fine." Asuka got to her feet and walked up to Rei, reaching out to touch her face.

Rei's hand shot out and grabbed Asuka's outstretched hand. "Do not touch me," Rei said with a low tone.

Asuka chuckled. "Ah relax. So touchy. I'm just trying to figure out what he sees in you. Up close, it's easy to see. You do have a very pretty face. Let's hope that's enough." With that, Asuka left, leaving Rei feeling more lost and confused than ever.

* * *

**December 16th, 2015**

Shinji slowly opened his eyes. The first thing that struck him was a sense of emptiness.

He sat up, groaning as his muscles that had gone unused for so long worked to lift his frame. Everything was blurry.

Shinji tried to say something, but all that came out was a croak.

Shinji felt a pair of arms suddenly wrap around his shoulders, and a face being buried in his neck. He couldn't see very well, what with being completely physically independent again, but he did recognize one thing.

Blue. There was a mass of blue pressed against the side of his face.

_Rei._

Shinji slowly brought his arms up to return her hug.

"Shinji..." Rei said quietly.

Shinji wanted to answer her. He tried to speak again, but nothing understandable came out. He huffed in frustration. Rei pulled back and stared at him with a hint of confusion. He tried to signal to her that his voice wasn't working, pointing at his throat and shaking his head. Rei stared at him in confusion.

Shinji slowly began to smile. He shook his head and pulled Rei back in for another hug. She seemed confused, before giving up and wrapping her arms around him again.

_It's good to be back._

**Notes for the Chapter:**

> And they're finally reunited!
> 
> Any comments are appreciated, and hang in there everyone! We'll all get through this coronavirus stuff, don't worry!
> 
> -AlphaBeta17 (3/24/20)


	4. Return to Reality

**Notes for the Chapter:**

> I refer to the fusion creature that is Godzilla and Eva Unit-01 as just Godzilla for simplicity's sake. Whenever someone in the story talks about Godzilla as he is at present, they are referring to the fusion creature, or the 'Sin From Genesis' as I call it.

**December 16th, 2015**

Misato sprinted down the hallways of Nerv, her breath coming in short, ragged bursts. She had just received word that Shinji had woken up.

She rounded the final turn and burst into Shinji's room. She stopped short at the sight.

Shinji's hands were clasped tightly in Rei's, and they appeared to be deep in conversation. They jumped at the sound of the door being thrown open and quickly moved apart. Misato stood for several seconds in silence before walking towards them.

"Shinji. I….I'm so, so sorry for what happened to you. It was all my fault, and-"

"No," Shinji said, cutting Misato off. She blinked in surprise. "It's not your fault Misato. None of it is. It's all my father's fault. He's the one who created the Evas. If Rei and Asuka's are both like mine, then they are in great pain."

Misato froze. _How does he know they're alive?_

Shinji continued on, his expression turning grim. "When I was inside the Eva, after….after I thought Rei died, a voice began speaking to me. It called itself the Evangelion, and it wanted to kill my father. Where is he by the way? I'd like to speak with him."

Misato looked at the ground guiltily as she digested Shinji's revelation. "Your father is gone. He ran off with Ritsuko and Ryoji. After the battle, the UN stepped in. The damage to Tokyo-3 was so catastrophic that they removed him from command of Nerv. I replaced him."

Shinji looked down as his breath started to quicken. Just the thought of his father was enough to get his blood boiling. "He needs to pay for what he's done. That coward. Running away like that. That bastard!"

Misato stepped forward. She wanted to embrace Shinji, but her status as Commander of Nerv meant that she felt she had to maintain some level of formality.

"I know. I want him to pay for what he's done as well. It's clear that he committed crimes against humanity with the creation of the Evas."

"What do you mean?" Shinji asked nervously. "Well," Misato said, not looking forward to telling Shinji what Gendo had revealed. "The Evas are organic monsters made from thousands of humans. Together, they created a monster that was contained by the armor plating of the Evas. That's why it 'spoke' to you. You woke it up."

Shinji sat back in shock, while Rei braced herself for Shinji's reaction to what she knew was coming.

"That's not all. Your father also claimed that….your mother voluntarily gave up her life to give life to the Eva. He claimed that she is the consciousness that is inside of it. If what you tell me about it 'speaking' to you is true…."

Misato took a deep breath. "Then you were speaking to your mother."

To Shinji, it felt like time ground to a halt. He sat there for several seconds without saying anything before he began to react. His stomach began to twist and contort, and he started to feel light-headed. "Help," he weakly said, before collapsing back into unconsciousness.

* * *

**December 17th, 2015**

"Shinji," Rei said as she entered his hospital room in the medical wing of Nerv, finding him already awake and staring out the window. He turned at the sound of her voice and a small smile broke out on his face.

"Hey, Rei. Thanks for coming to see me," he said. She walked over to stand beside him, and noticed that he was leaning against the window. "Do you need help," she asked. Shinji nodded in response. "Yeah. It took me a while to get over here, could you help me back to my bed?"

Rei silently nodded and helped him back to his bed, where she sat down beside him. They sat quietly together for several minutes before Rei finally broke the silence.

"How are you doing," she asked, hoping not to upset Shinji. She figured that he would be in a lot of emotional turmoil right now, and that maybe getting him to talk about it would be the best way to help get him back to normal.

"Honestly, I don't know. I don't know how to feel about my mother possibly being alive. I don't know how to feel about her maybe being inside the Eva, and being the one that I fought Godzilla with. The Eva was the one that chose to merge with Godzilla. After we were….eaten, it told me that it was fighting back. That it wouldn't accept being dead. How should I feel about that? It didn't sound like my mother, or at least, not what I remember of her. I don't even remember what she looked like. It's more of a feeling, an emotion, than anything."

Rei wasn't sure how to respond to that, so she tried asking another question. "What do you know about the Eva?"

"Besides that it hates my father? Not much else. All I could tell is that it was full of anger. When I was fighting alongside it, it felt like I wanted to destroy everything. Rip everything apart. It was…."

Shinji looked down at his hands and slowly opened and closed them. "It felt good. That scares me, Rei. I don't want to become my father."

"Shinji," Rei said. He turned to look at her. Her expression took on an earnest note as she tried to think of what to say. "I still do not know much, but I do know this. You are not your father. You never will be. You were kind to me, which is the opposite of how he treated me. He would tell me that I only existed to serve him, and that I didn't matter otherwise. Then you came and told me how I did mean something. You tried to be my friend, and helped me start to become my own person. Please. Believe me. You are not your father."

Shinji couldn't help but smile. "Thank you. That means a lot." A thought occurred to him.

"What was your mother like?"

Rei looked surprised. "I…." She looked down. "I never knew my mother," she quietly said. "I spent my whole life that I can remember being raised by your father. He told me that my parents were dead, and that he took me in." Rei's voice began to falter. "I….wish I knew what it felt like. To have a mother." She felt the quickly-becoming-familiar emotion of sadness start to creep its way through her. It filled her red eyes, and Shinji couldn't help himself. He reached out and pulled her into a hug. She wrapped her arms around his thin frame and they held each other for several minutes.

"Thank you," Rei said. "For what," Shinji replied.

"For coming back. For not being dead."

* * *

"I'm sorry for springing that information on you like that yesterday, Shinji," Misato said.

"It's OK. I'm glad you told me, all things considered. It's probably not true anyway. My father's crazy, after all. He _wanted_ the Eva to go berserk? That was his goal? And he thinks that there's some extra-terrestrial threat coming to destroy Earth?"

"Yeah, it sounds pretty crazy," Misato admitted. She wasn't sure herself that there wasn't a shred of truth to what Gendo had revealed to her, but she wasn't about to tell Shinji that. He appeared to be at ease with Rei by his side, and she didn't want to destroy his good mood.

Unfortunately, she had something to tell him.

"Shinji," Misato said. He turned to face her again. "You can take a few days to rest and recover, but I'm sorry to tell you, then we'll need you back here at Nerv. We need to start conducting research on Godzilla and how to control it with the Eva as soon as possible."

The smile fell off of Shinji's face. "What?"

Misato sighed. "I don't think I can soften this. We need you Shinji. Biollante was the first monster to attack us since Godzilla back in October, and without you and Godzilla, we would have lost. We need you to learn how to use this newfound power to our advantage."

Shinji shot to his feet in anger, but collapsed, his legs unable to support his body. Rei reached out and helped him stand while he glowered at Misato. "You can't be serious. You can't expect me to get back inside Godzilla! Not right after getting out!"

"It won't be right away Shinji, but yes, we will need you to. If you don't then what's left of Tokyo-3 could be destroyed. We still don't know why we're being attacked by these monsters, but until they stop, we need you, as well as Rei and Asuka, to pilot for us."

Shinji stared at Misato with a growing sense of betrayal. He began to try to walk out of the room, aided by Rei. Misato held out her arm to stop them. "No, you can't leave, you need to rest-"

"No!" Shinji yelled, anger sparking in his eyes as he pushed past Misato and began to make his way down the hallway with Rei. Misato was about to go after them, but stopped herself. She turned back to the empty room and sighed.

_I hate having to do this to him, but he's necessary to the survival of Tokyo-3, whether he likes it or not._

* * *

Makoto stood up to greet Misato as she entered Central Dogma. "So how did it go?"

Misato shook her head. "He didn't take it well."

Makoto shrugged. "I don't blame him. Who would want to get back inside that monster? I know I wouldn't." He paused before hesitantly pushing ahead. "Are you sure it's a good idea to not tell the pilots about the object that just entered the solar system? Our astronomers just reported that it's on a direct course for Earth, and will probably arrive in a couple of weeks."

"I know. But if I told them, it would probably be counter-productive. We have no idea what it is, so the best option is to continue as normal until it gets here. We'll start training with Shinji as soon as we can, and see if having Godzilla under our control will be enough. It was for Biollante after all, and Miki thinks that perhaps Shinji and the Eva can 'work' with Godzilla. Meanwhile, see if you can get Daisuke going on Orga's regenerative DNA. The faster we can get it working, the better. Besides, now that the UN has granted us ownership of Godzilla, maybe its own regenerative DNA could prove useful."

With that, Misato turned and walked out, leaving Makoto to mull over the new developments.

"Is she gone?"

"Yeah, you can come out now," Makoto called out. Miki and Daisuke crawled out from under their desks, both having been hiding while Makoto tried to 'reason' with Misato.

"I still think you're crazy for trying to change her mind," Daisuke grumbled. "Believe me, she wasn't always like this," Makoto responded defensively. "She's just been under a lot of pressure ever since you guys got here. She used to be way more easy-going and laid back."

"Hah! According to the technical staff, she was always crazier than you," Miki quipped.

"Thanks, Miki," Makoto sarcastically said. "Are you sure about Godzilla?"

"Of course! It wouldn't have been able to fight off Biollante successfully without at least some level of cooperation between itself and the Eva!"

"But we don't even know if the Godzilla that attacked before still exists! It might just be Shinji and the Eva working together to control Godzilla's body now," Daisuke stated. "Its own consciousness, if you could even call it that, could have been destroyed in the fusion process with Unit-01."

"But you yourself said that 'we can never be certain about anything in science' and so I'm not ruling this out! I've got a gut feeling about this," Miki proudly responded.

"That may be so. But it doesn't change the fact that we don't know how we're going to survive the incoming extra-terrestrial threat!"

Miki's defiance faded away as Daisuke's statement brought her back to the true threat. "You're right. I hate to admit it, but we don't know what we're going to do." Miki turned to Makoto. "Nice try anyway with Misato. It makes no sense not telling the pilots, but she is the commander."

"Yeah," Makoto gloomily said. He didn't tell Miki or Daisuke, but he was becoming increasingly concerned about Misato. Keeping secrets was much more in line with what Gendo would have done.

* * *

Asuka was waiting at Rei's front door when Shinji and Rei finally reached Rei's apartment.

"Ah, hello there!" Asuka said cheerily. Shinji groaned, already exhausted from the train ride from Nerv. "Not now, Asuka," he groaned.

"Aw, really? I haven't seen you in over two months! Look at you, you're even skinnier than before!"

Rei glared at Asuka as she shoved past her and opened the door to her apartment, pulling Shinji inside with her.

"Hey wait, you can't-"

SLAM

"Thanks," Shinji said, already looking like he was about to collapse. Rei led him over to her couch and he immediately laid down, falling asleep almost instantly, his body exhausted from the exertion. Rei stared down at him while Mari came trotting up to them, jumping up onto Shinji and sniffing his head. After a moment, the now several-month-old cat yawned and curled up on his chest, seemingly oblivious to Shinji's absence.

Rei watched the one-eyed cat's behavior with confusion before accepting it as yet another weird quirk in non-human behavior.

* * *

Misato opened the door to her apartment and walked in briskly, looking for Shinji.

"Hello? Shinji?"

Asuka's voice filtered through from her room. "He's at Rei's!" Misato shook her head, not surprised. Asuka came out and folded her arms, staring at Misato. "He didn't like being told that he's going to have to keep piloting, did he." It wasn't even a question.

Misato sighed. "Yeah. I feel bad for him. He's just a kid. Having to go through all that, and to finally escape, only to be told he's being thrown right back in..."

"Don't beat yourself up too badly. Remember, this is Shinji we're talking about."

Misato groaned. "OK. Out with it. What the hell is so bad about Shinji? You've had it out for him ever since you got here."

Asuka stopped and thought about it for a moment. "He's just so...infuriating! It drives me crazy! Always moping around, being all quiet, and whining about having to pilot a freaking Eva!"

Misato shook her head. "Asuka. Has it ever occurred to you that maybe Shinji doesn't like piloting his Eva? Especially now that it's some weird fusion with Godzilla, and if Gendo isn't lying, that his mother is inside of it? Think about that for a minute. What would you do if your mother was inside your Eva?"

Asuka scoffed at the notion. "But she isn't. She'd never do anything like that anyway. She went all psycho and ended up killing herself. The bitch."

"Asuka, are you sure you don't want to talk about that?"

"NO! Of course not! What are you, stupid? Why would I want to talk about my dead mom who rejected me in favor of a stupid doll and killed herself because my dad cheated on her? No really, why? Besides, you hate me. You attacked me just because I said what was true: you wish I'd been the one eaten by Godzilla, not Shinji. You just like him because he rolls over and takes whatever shit you make him do!"

Misato almost launched herself at Asuka, but managed to stop herself this time. She pressed her fists into her forehead and tried to take deep breaths. "Just go away Asuka. Whenever anyone tries to reach out to you, you just push them away. Maybe that's why you seem to be so fucking depressed, despite how much you try to hide it!"

That statement hit close to home for Asuka, and she lashed out one final time in anger. "And maybe I am! A lot of good you're doing, having to restrain yourself from attacking me! It's a good thing you don't have any real kids, they'd probably be dead by now!"

It was as if Asuka had smashed a brick against Misato's head. She staggered and collapsed to the ground, memories of the aftermath of surviving ground zero for the Second Impact flooding her mind. How the doctor had had solemnly told her that the internal damage would-

"You know what? Fuck you! Get out! Get out of my home! NOW!"

Misato scrambled to her feet in a fit of rage and chased the redhead out of her apartment, slamming the door behind her and collapsing against it. After trying to hold in her tears, she finally cracked and began to sob at what she had just done.

* * *

Shinji opened his eyes and found himself in Rei's dimly lit apartment, moonlight streaming through the window nearby. He tried to move but found he was held in place by Mari, who cracked her one good eye open to stare at him for a second before closing it and going back to sleep. Shinji could have moved her off of himself if he wanted to, but he didn't have the heart to do it.

"Rei?" Shinji quietly called out. After several moments, sounds of movement came from her bedroom, and her door opened. She came out looking exhausted. "Did I wake you?"

"No," Rei responded, rubbing her eyes. "I have been having trouble sleeping ever since Godzilla attacked the second time. Whenever I fall asleep now, I have dreams. I didn't use to have those."

"What do you dream about?"

Rei shivered. "A three-headed dragon."

Shinji felt like he had been struck by lightning. A memory flashed in his mind's eye for a split second. He gasped aloud, startling Mari, who indignantly jumped off him and trotted off to find somewhere else to sleep.

Shinji sat up and slowly asked Rei a question he didn't want to know the answer to. "Rei. Was it golden?"

"What?"

"The three-headed dragon. Was it a gold color?"

Rei hesitated, confused, before answering. "Yes. How did you know that?"

Shinji's mind whirled. "I think I've seen it. I can't remember where though. Maybe it was...no. It couldn't be."

Rei sat down next to Shinji. "Where?"

"Back during one my Sync tests, before we were friends. I blacked out and had a dream. I can hardly remember any of it, but something just came back to me. An image of a giant three-headed golden dragon."

Rei contemplated the information. "Do you think it is connected to my dreams?"

"I don't know." Shinji sounded forlorn as he leaned forward and put his head in his hands. After a moment, he sat back up and turned to Rei. "Do you know where my SDAT player is?"

Rei looked surprised, but she knew the answer. "I have it. After you were taken by Godzilla, I asked Misato if I could have it, and she said I could. I can give it back to you if you want."

Shinji shook his head. "No, but would you mind going and getting it?"

Rei nodded and went into her room, returning after a moment with the music player. She sat back down next to Shinji and looked at him.

Shinji smiled. "Here. Let's listen to Claire de Lune. Like the night before Godzilla attacked."

Rei looked surprised, before handing the player to Shinji. He plugged in the earbuds and handed one to Rei, putting the other in his own ear. He navigated to the song on the tape and pressed PLAY.

The plaintive yet hopeful piano notes filled their ears as Shinji and Rei sat together, listening to the song together once again.

**Notes for the Chapter:**

> There's a lot of character threads running through this chapter, and I hope I managed to display them all pretty well. I've been trying to display Rei's growth as a character all this time by slowly having her open up more and accepting Shinji's friendship. Shinji is recovering from his experiences, and continues to grow closer to Rei. Asuka meanwhile just had a massive paradigm shift, and I have some interesting plans for her story moving forward. Misato is intentionally being contrasted with Gendo as she tries to not become like him, while more allusion to Ghidorah's eventual arrival is spread throughout the story.
> 
> I hope you're all enjoying this so far!
> 
> -AlphaBeta17 (3/31/20)


	5. Descent into Madness

**December 21st, 2015**

Godzilla charged forward, making good use of its slender Evangelion legs. Reaching out with its humanoid hands, it grabbed the octopus-like monster Gezora around the midsection and squeezed, spurting blood out of the monster all over itself. Godzilla roared in triumph as it dropped the lifeless body to the ground and continued on with its rampage.

Misato shook her head in exasperation. "It's like he isn't even listening to us."

Inside Godzilla, Shinji grinned maniacally as the influence of both the Evangelion and Godzilla took control of his mind, battering his naturally peaceful inhibitions to pieces. Despite having undergone mental preparations with Miki beforehand, as soon as his Entry Plug had been inserted into the back of Godzilla's neck he had been out of control.

"Slow down! Wait for Rei!" Misato yelled in frustration as Shinji once again surged ahead and grabbed the imaginatively named Giant Sea Serpent that was twisting its way around one of the last skyscrapers in Tokyo-3.

The poor reptilian monster barely had time to gasp in agony before Godzilla pulled it straight through the building, grabbed both the upper and lower halves of its jaws, and ripped it in half, splitting the monster down the middle.

Even Daisuke looked mildly distressed at the violent display. "The sheer power this hybrid possesses….it's terrifying," he solemnly stated.

"No," Makoto said. "None of this would be possible without Shinji."

**Earlier that day….**

Misato groaned at the news. "Seriously? Seven monsters, all converging on Tokyo-3 at once?! Give me a break! How did Gendo not go crazy having to deal with all this?!"

Makoto raised his eyebrows behind Misato's back at the irony in her statement.

"Well, so far they're each completely independent and appear to not be cooperating at all, which is a plus for us," Miki stated as she scanned her bioacoustic devices. "I didn't pick up any particularly significant increases or decreases in frequency, so for now, my theory about the monsters being attracted by a bioacoustic emitter remains unsupported by the data."

"A pity," Daisuke mumbled to himself. "On a more important note, it appears that all seven of these monsters are essentially giant, radioactive versions of regular animals. If I had to make a guess, I'd say they were created the same way Biollante was."

"And what way would that be?" Misato asked.

Daisuke's expression turned grim. "Purposeful chemical experimentation. Probably by your previous commander, Gendo. This attack will be too much for Rei to handle by herself. We'll need to sortie Shinji in Godzilla. Unless, of course…."

"No. Asuka has been stripped of all Nerv credentials, and her Eva is locked down indefinitely. She's gone. Someone fetch Shinji. I need to have a word with him."

After a moment, Daisuke spoke up again. "I saw him wandering around with Rei."

"Great. I'll be right back." Misato spun on her feet and stalked off to find the boy while Miki turned toward Daisuke in anger. "You gave him up! Just like that?"

"Yes," Daisuke replied. "It gives me no pleasure, but we need him to pilot."

"But what about his mental health?" Miki cried.

Daisuke sighed. "That's probably the least of our concerns right now."

Misato approached Rei and Shinji carefully. Ever since she had kicked Asuka out of her apartment in a rage, the other two pilots had been avoiding Misato. Not only that, but Shinji was still furious with Misato for telling him that he would have to conduct tests on Godzilla in his Entry Plug. They hadn't done any yet, but now, there was no choice. Shinji would have to pilot, whether he wanted to or not.

"Shinji? May I have a word?"

Shinji glared at Misato while Rei stared blankly at her, standing protectively by Shinji's side. "No. I won't do it. I'm sorry, but I just won't."

Misato stood silent for a second before barking out an order.

"Rei. Go get changed into your Plug Suit and report to your Entry Plug."

Rei didn't move. Misato's expression hardened.

"Now!"

Years of conditioning kicked in. Rei gave Shinji a small but silent apology before walking off, leaving him to face Misato alone. He tried to muster up his courage to continue onward, and shook his head vehemently. "No! I'm not getting back in that thing! Not after I just woke up a few days ago!"

Misato groaned. "Don't make me do this, Shinji. Just shut up and go change into your Plug Suit."

Shinji felt fear sweep through him at Misato's tired tone. Nobody had seen Asuka for several days, and her last known location had been Misato's apartment. Shinji didn't like the red-head, but he didn't wish harm upon her. That was exactly what everyone feared had happened, however.

Shinji took a deep breath. "Misato. I can't. I just….I can't. Please, don't make me do this. Please!"

Misato felt a pang strike her heart at the young boy's pleading tone. She pushed the feelings down and drew her face into a snarl. She grabbed Shinji by his shoulders and shook him. "We don't have time for this! There are seven monsters out there! Rei won't be able to handle them by herself! Stop whining and get in the goddamn Entry Plug!"

"No!" Shinji's voice was quickly filled with panic. "There's no way I'm going to voluntarily put myself back into that situation!"

Misato huffed in anger. "Shinji. I know you're trying to stand up for yourself more. That's all well and good, but that doesn't mean continue to hide from your responsibilities!"

Shinji's eyes flared as anger swept through him. "No! I'm sorry, but I'm done being told what to do!"

Before he could say anything else however, Misato had grabbed him by the front of his shirt and yanked hard on it, pulling him with her as she marched down the hallway to the locker room.

"If you won't get yourself changed in the next five minutes I will personally strip and shove you into your Entry Plug myself!"

Shinji's shirt tore as he fell backward onto the ground, leaving him feeling defenseless as Misato stood towering over him with absolute authority. "Get moving, you little brat," her voice growled out. As Shinji cowered at her feet, Misato felt a surge of power flow through her. Coupled with feelings of disgust towards the boy that she had long since decided were false after seeing him in battle quickly resurfaced.

"No…." Shinji whimpered one last time.

Misato reached the end of her patience and drew back her hand.

Makoto had to look away as Godzilla dispatched the crab monster Ganimes by ripping off the monster's claws and stabbing it with them. It was no wonder really, considering the beating that Shinji had supposedly just received.

Several minutes after she had left to go find Shinji, Misato had returned and tonelessly told Miki to go 'prep Shinji mentally' before the battle. When Miki had come back a while later, she had cautiously pulled Makoto and Daisuke aside and mentioned that Shinji's face and upper body had been covered with bruises.

Daisuke flinched as Godzilla flipped the turtle monster Kamoebas onto its back and tore into its belly with its atomic breath, baking the creature from the inside.

Miki quietly told Rei to stand down. The blue-haired girl had been sortied along with Shinji, but her Eva had frozen in place after he had wordlessly charged ahead and began fighting the monsters one by one, her Prog Katana dandling uselessly at her Eva's side. Rei didn't move until Godzilla turned its atomic breath on the aptly named Giant Octopus. With a single strike of the green beam, the monster imploded, spraying bloody ink all over a large section of Tokyo-3.

Rei turned her Eva around and sprinted back to Nerv, ducking behind the giant steel pyramid and peering out from behind it.

It made Makoto sick looking at Rei cowering in fear from the gentle boy she had grown so fond of. He had never really gotten to interact with Rei before Shinji arrived, with any attempt to make conversation with the mysterious girl resulting in a blank stare. After Shinji began spending time with her however, Rei had slowly begun to respond to his queries. It had been a momentous day when she had accepted his offer for a soda when she walked past him while he was at the vending machine.

'Shinji believes I should try more things,' she had bluntly stated, before pointing at the Coke symbol on the side of the machine. Makoto had chuckled and thumbed in the couple of dollars into the machine, which promptly spat out the red can, which he handed to the girl. After a moment of staring at it, she had looked back at him expectantly.

'Oh! Sorry, it works like this,' and he had shown her how to pop the pull tab. She had taken a sip immediately. 'It tastes….good,' she had said, and started to walk off before turning back to him. After a moment of hesitation, she had quietly said 'please….don't tell Commander Ikari.'

Makoto remembered how he had chuckled and winked at the girl. 'Don't worry, I don't like him very much either.'

Rei had stared at him with a strange expression before turning and walking off. An odd exchange to be sure, but it was progress, and Makoto was sure that Shinji's influence was the spark that had started it.

Now, watching as Godzilla viciously ripped the wings off the praying mantis monster Kamacuras, he felt a growing sense of disgust build as he glanced over at Misato, who was now watching the carnage unfold silently.

In the deserted center of Tokyo-3, Godzilla turned and roared at the sky, mixed once again with the bellow of the Eva and Shinji's screams. Makoto shivered as his skin crawled at the sound that was never meant to be heard.

Godzilla charged at the final monster, the lobster-like Ebirah, which screeched and lashed out with its giant pincher claw, which snagged Godzilla's tail and snapped it clean off, causing the hybrid to tumble onto the ground while the crustacean climbed on top of it and began biting at Godzilla's dorsal plates.

Godzilla roared and with a blast of light ignited rows of green beams out of its back, slicing through Ebirah and killing it instantly. As Godzilla got to its feet, its tail was already regenerating, and after a moment, it stood proud and tall, without a scratch on its deformed mess of a body.

Miki sighed. "This is truly horrible. I see now why your former colleagues left, Makoto."

Makoto shook his head. "It was bad….but never to this extent."

"Shinji appears to have lost his self-control, unleashing the monster that exists inside all of us. Even Shinji," Daisuke uttered, "the gentle young one, falls when he is pushed over the edge."

**December 22nd, 2015**

Shinji lay on his bed with his arms flung over his head as he tried to quiet the screaming voices in his head.

_ You're a monster, Shinji. _

_ Why are you so stupid? _

_ Just shut up! _

_ Go cry in a hole! _

_ You little brat! _

_ What did you do out there? _

_ You killed so many people today. _

_ What's wrong with you? _

_ What's wrong with you? _

_ You're a monster, Shinji. _

_ What's wrong with you? _

_ What's wrong with you? _

_ WHAT'S WRONG WITH YOU, YOU MONSTER! _

"GO AWAY!" Shinji screamed as he grabbed his alarm clock and threw it across the room, where it smashed against the wall and fell to the ground. He clasped his hands over his ears as he squeezed his eyes shut, trying to forget Rei's face when she had finally opened the door to her apartment after the battle. After recovering from the shock at the bruises on his face, her expression had gone back to its blank state that had occupied her face all the time when he had first met her.

'Rei, please, I'm sorry-'

'I do not want to see you right now.'

'No, please, it wasn't my fault, I-'

The door had slammed shut in his face, along with his hopes of finding solace with what felt like his only friend. He had grabbed the doorknob before she could lock it and tried open it again, only for her to suddenly swing it open and punch him in the face, the blow sending him backward and allowing her to slam the door shut and lock it.

"Shinji?" Misato's voice rang out as she knocked on his door. For a brief second the memory of what had happened to him at her hands after he refused to pilot returned to Shinji, and he shuddered.

"Go away," he called out.

After a moment, he heard Misato sigh and walk away.

Asuka sat up in her hotel room bed and yawned before getting up. She had been siphoning off money from her Nerv card ever since she arrived in Tokyo-3 and had a personal card with several thousand dollars on it that she had fortunately had on her when Misato had kicked her out.

The first two days had been rather boring for her. Since her Nerv card had stopped working, she assumed that meant she was no longer employed for them, which meant she had no incentive to continue to go to school. It also meant she could no longer pilot her Eva. She had raged around the room, throwing stuff at the walls while she fumed in anger at Misato, Rei, Shinji, and really, well, everyone, before calming down and trying to figure something out.

While there had been several moments where she had considered some dark options, ultimately, her narcissism had won out. She had gone out onto the streets and searched for someone. In the end, she had found him.

"Mr. Kaji! What's on the docket for today?"

"Well, for starters, great job with those monsters yesterday! All seven were big enough to be able to fight Godzilla, and all seven were easily dispatched by it," Ryoji stated as he smirked at the young girl.

"Well of course! I am a genius!"

Ryoji laughed. "Yep, you are," he said, as he internally patted himself on the back for the genius in taking advantage of Asuka's admiration for him. As soon as he had heard from the pipeline that Asuka was kicked out of Nerv, he had made sure to make himself as conspicuous as possible on the streets of Tokyo-3, and sure enough, Asuka had come looking for him.

In the end, he had managed to get Gendo and Ritsuko to agree to incorporate Asuka into their plans. Well, partially. They didn't tell her about their true intentions of course. Only that they were looking to take back control of Nerv, and that if Asuka helped them, she could get her Eva piloting job back.

'Helping them' had consisted of applying Ritsuko's chemicals to the seven animals. A lobster, a crab, a sea serpent, an octopus, a praying mantis, a turtle, and a cuttlefish. It was a dangerous task, and so naturally Asuka had jumped at the opportunity to do it.

"So what now?"

"Well, Ryoji said as he sat back in his chair as he munched on some chips. "We're planning on infiltrating Nerv on December 31st, in the evening, when there will be almost no security. Even though you are no longer a member of Nerv, if you go to the front gate and plead with the night guards, there's a good chance they'll let you in if you tell them you want to pick up a few things that you 'left in your locker' and from there you can let us in at another entrance. We'll get to Central Dogma and activate your Eva, which you will of course pilot, and then we'll force the UN to hand control of Nerv over to us!"

Asuka grinned. "Sounds like a plan!"

**December 24th, 2015**

Shinji nervously knocked on Rei's door and stepped back. He took a deep breath and braced himself.

After a couple of days of mental torment, he had decided to make one last appeal to Rei. If he failed….he planned on running away from Tokyo-3. There was no point in staying in his mind. The city was almost empty anyway.

The door slowly opened and Rei's cautious expression peered out at him.

"Yes, Ikari?"

Shinji fumbled with his words as he spoke, trying to ignore the spike of pain at hearing her refer to him only by his last name. "Yes, hi, um…."

After a moment of awkward silence, he restarted his sentence.

"Rei, I want to apologize. For everything. Could you let me in so we can talk?"

After a moment, Rei's expression softened and she swung her door open.

"OK."

"Thanks," Shinji said as he came in, Rei shutting the door behind him and going to sit on her couch, Mari curled up asleep next to her. She stared at Shinji expectantly while he took a deep breath and began, standing in front of her.

"Rei, I'm sorry. I'm sorry for losing control out there. I was blaming everyone besides myself for it, but as I thought about it, I realized that maybe it wasn't everyone else's fault," he began. Rei's expression didn't change, so he pushed on.

"I saw a side of me out there yesterday, and I didn't like it. It scared me, Rei. It scared the hell out of me. After Misato….beat me for refusing to pilot, I gave in to my anger while I was in Godzilla. As soon as my Entry Plug was inserted, I felt a huge rush of anger coming from the Eva. I don't know what that means. Maybe it is my mom, I don't know. Either way, I embraced it and allowed it to take over. Along with the natural anger of Godzilla, I became….a monster."

Shinji bowed his head in shame, not able to bring himself to meet Rei's eyes.

"I caused so much unnecessary destruction out there. Even though the city is mostly empty now, I still ended up killing people. It's my fault those people died. And the way I fought was just inhumane. It was barbaric. It was…."

Shinji sighed. "It was madness. I went mad out there, and I didn't fight it. At the time, I liked it. It felt good. I was angry, and I lashed out in my anger, and I hurt a lot of people. Looking back, I realized what I allowed to happen, and I'm ashamed."

Shinji felt tears prick the corner of his eyes as he tried to finish. "And when all that was done, I found out just how much I scared you. When I came to see you, I tried to force my way in. I didn't give you space, and I'm sorry for that. You are your own person, and I need to learn to respect that."

Shinji wiped his face as he finished. "I'm sorry, Rei. I'm sorry. I understand if you don't want to be around me anymore. I won't try to insert myself into your life. I'll go if you want me to go."

After a moment of silence, Shinji's heart sunk.

"OK. That's OK. I'll just….I'll just go then-"

"Shinji?" Rei quietly asked.

Shinji felt his heart stop. He looked up and was shocked when he saw Rei's tears.

"Yes?" He responded.

"Can you….can you come hug me?"

Shinji was dumbfounded at Rei asking for a hug, but he wasn't about to turn her down. After only a moment of hesitation, he came forward and wrapped his arms around her.

"Thank you," he quietly said. Rei only responded by squeezing him tighter.

**Notes for the Chapter:**

> There's a lot of stuff I tried to do with this chapter, and I really hoped it all worked together. The next chapter will be a bit happier though, don't worry, and will mark the halfway point of the entire Evangelion X Godzilla story! I might try and actually get it out on Friday evening, but we'll see!
> 
> Thanks for reading, and comments are always appreciated!
> 
> -AlphaBeta17 (4/7/20)


	6. Moonlight

**December 24th, 2015**

"Misato….hit you?"

"Yeah," Shinji said as he and Rei walked down the empty streets of Tokyo-3. It was dusk, with the sky rapidly fading from the orange of sunset to the darkness of night. Puffy clouds dotted the sky, reflecting the vanishing sunlight to create a beautiful array of colors.

"She should not have done that," Rei said with a tinge of bitterness in her voice. "Just like I should not have hit you."

"Well, I did kind of deserve it…." Shinji began, only to be stopped by Rei, who held out her arm to block his path, leaving him staring breathlessly into her crimson eyes.

"No. You did not. I….apologize for hitting you." Rei's voice was solemn as she struggled to convey her guilt.

Standing this close to her, Shinji was reminded just how emotionally immature Rei was. He couldn't fault her for it, and at this point, he didn't really care. She was his friend, and that was all that mattered.

"It's OK, Rei. I know you would never do anything to hurt me," Shinji said as warmly as he could, trying to help her understand that he wasn't upset with her. "You were scared of me, and for good reason. When I was inside Godzilla, right after Misato beat me, I gave in to my emotions, and I caused a lot of pain. I shouldn't have done that. I understand that now."

Rei looked down at the ground. "We should not give in to our emotions?"

"Well," Shinji stated, halting briefly when he saw Rei's expression drop slightly. "There's nothing wrong with emotions, they're what make us human. It's how we use them that matters."

Rei nodded slowly, and Shinji scanned their surroundings. He gestured towards a nearby park, and the two children went and sat down on a bench overlooking a small pond. Neither said anything, both adrift in a sea of feelings that neither realized the other was also lost in. As the night slowly grew darker and darker, Shinji noticed that Rei seemed to be somewhat nervous.

"Are you OK?"

Rei slowly turned her head to look at Shinji, her expression unreadable. "I am confused," she said. "I feel something, and I do not know what I should do with it."

Shinji felt his breath catch in his chest. "What do you mean?"

Rei stared at the small pond as she gathered her thoughts. After several minutes, she began to speak. "Ever since you began talking to me, I have been changing. I feel….more awake than I ever have. Before, I was doing only what I was told to do. If Fuyutsuki told me to go home and lie down, I would do exactly that. If Ritsuko told me to strip and let her poke and prod me, I would let her. If your father told me to stand still and let him stare at me for a while, I had no choice. I would do it. I never cared. All I was….was Rei Ayanami."

Shinji was about to say something, but Rei put her hand on his shoulder, and shook her head. Shinji nodded, deciding to remain silent. Rei had spent her whole life being told what to do. The least he could do was let her speak.

Rei didn't remove her hand as she continued.

"Then, you. You came to Tokyo-3. You brought a softness I never thought someone like me would experience. You became my friend. You were nice to me. You talked with me, even though I did not talk much. When I shut you out these past days, I wanted to be near you. You treated me like a person, and allowed me to make decisions. When you offered to let me take care of Mari, you did not force me to do it. You said you thought it would be good for me, so that I would not have to live alone."

Shinji thought back to that conversation, back before he and Rei fought side-by-side against Anguirus, Baragon, and Varan. He had suggested it after Rei met Mari, and was fascinated by the young one-eyed black cat.

"Nobody had ever done something like that for me," Rei continued. "Why would you?"

Shinji was taken aback. "Because you're my friend."

"Why are you my friend?"

That stopped Shinji. "Because you're kind, and thoughtful, and you never give up, never! I've always struggled with running away, but you're always so, so brave. And you don't mind that I'm skinny, or scared, or that I make mistakes. And you're strong, and beautiful, and..."

"And...?" Rei questioned, seemingly hoping for a certain answer.

"Well, yes, and..."

Shinji took a deep breath. _I can't hold it in any longer. Screw it. I'll just say it and deal with the consequences._

"...I'm in love with you." Shinji looked away in shame. "I'm sorry, Rei. I'm sorry. But that's how I feel about you. I think a part of me has always felt that way, ever since you fought off those bullies, and dragged me to your apartment. Apartment 402. I still remember. It was filthy. I tried to clean it, and you asked me why. I never ended up responding, since you said my father told you not to talk unless necessary, and I objected to that. I guess I'll answer your question from back then," Shinji said slowly. "I wanted to clean your apartment because you were nice to me, and I wanted to be nice back to you."

Shinji jumped when he suddenly felt Rei's hand on his shoulder move. She turned him back towards her, and Shinji shut his eyes, scared to death of what her expression would be.

When he felt her warm lips brush against his, he let out a gasp of air, causing her to pull back, startled. Shinji opened his eyes to find Rei uncharacteristically blushing.

_She looks….embarrassed?_

"I apologize," she began. "I don't know-" Rei was cut off when Shinji closed the gap again and gently pressed his lips against hers. He didn't know what to do, so he left his hands dangling by his side while his heart pounded, about to burst from anxiety.

After several long seconds, they pulled apart and stared at each other in shock.

Shinji had no idea what to say, and instantly regretted the first thing that popped out of his mouth.

"You taste better than Asuka did."

Rei blinked.

Shinji's face took on a horrified expression. He was about to start rambling apologies when Rei suddenly giggled.

_She's giggling. Wait, what?_

Rei's giggles quickly morphed into a soft laughter that brought a smile to Shinji's face. After a moment, he chuckled as well.

"Maybe that wasn't the best thing to say?" Shinji remarked, which only set Rei off again. After a moment of confusion, Shinji gave up and started laughing with Rei. Neither of them noticed as the moon peaked out from behind the clouds.

* * *

**December 25th, 2015**

The next morning, Shinji knocked on Rei's apartment door, and after only a few moments, it swung wide open.

"Hey, you ready to go?"

Rei softly smiled at him. "Yes."

She reached out and took his hand, bringing a blush to his face. While this was rather new to him, he imagined that it was even more outside the norm for Rei.

_I still can't believe we're….dating?_

Shinji even wasn't sure it could be called dating. After the kiss, they had spent some time quietly talking before making their way back to the apartment building. At Rei's door, he had asked her if she wanted to spend the next day with him. She had said yes.

That night, for the first time in a long time, Shinji didn't lay in bed struggling to sleep due to his anxiety and fear. Instead, he struggled to sleep due to excitement for the coming day.

The next morning, when he had left the apartment, Misato had tried to stop him in order to talk.

'Shinji, listen-'

'Bye Misato,' he had quickly said, shutting the door behind him.

"...And I brushed her off, just like that," Shinji told Rei.

"You would not have done that several months ago," Rei remarked. "You have grown."

"So have you," Shinji said as he blushed. "You're way more talkative now, and you've been making more decisions for yourself."

"Such as?"

"Well," Shinji started, a small grin crossing his face. "You kissed me last night."

"Ah, yes. That did happen."

Shinji gave Rei an incredulous look. "Was that intentionally sarcastic?"

"No," Rei said as she looked straight at Shinji without blinking. After a moment, Shinji noticed the corners of Rei's mouth twitching upward, and he burst into laughter while Rei allowed a small smile to cross her face.

* * *

"What is this?" Rei asked as she examined the strange red and white dessert. The two were sitting together on the same bench from the night before, overlooking the same small pond.

"It's strawberry shortcake," Shinji said as he took a bite. He was having an early lunch with Rei, consisting of snacks he had purchased at a nearby convenience store. The one he had saved for last was the dessert in question.

"It's good," he said. Rei gingerly speared a piece from the small box they were sharing with a fork and tried it. Her eyes widened slightly.

"You are correct, it is good," she said as she took another bite.

Shinji chuckled as she dug into the sugary treat. "Hey, don't eat all of it, save some for me!"

Rei's eyes flashed with what only Shinji could have identified as humor as she pulled the box closer to herself. "You said I am making more decisions for myself than I used to. I have decided to take this strawberry shortcake and eat it myself." In an apparent act of defiance, she took yet another bite.

"Rei….are you making another joke?" Shinji asked with a slightly bemused expression.

"No, I am not joking, Shinji," Rei said as she swallowed her bite and took another. "What ever gave you that idea?"

It was her delivery that managed to be even flatter than how she used to normally talk that clued Shinji in to her sarcasm. That, and how her expression suddenly took on an innocent note, as if to say 'who me?'

Shinji groaned lightheartedly. "Nothing, nothing whatsoever."

Rei's eyes widened slightly. "I'm sorry if I confused you," she said seriously.

"Oh no, don't worry," Shinji said as he shook his head. "I was being sarcastic as well."

"Oh," Rei said as her expression dropped. "I didn't realize."

"Hey," Shinji said softly as he decided to be bold and reach out to clasp Rei's chin, angling her face towards him. "Don't worry about it. You're new to this, you'll pick it up over time, don't worry," he as he looked into her eyes and tried to convey his care for her.

After a moment, Rei's expression lifted. "Thank you," she said. She surprised Shinji by leaning forward and pecking him on the lips, leaving him a blushing mess. As Rei leaned back, her eyes took on a twinkle. "It appears that kisses are the quickest way to startle you. I shall remember that."

* * *

Shinji cracked his eyes open and was nearly blinded by the sunlight.

_That's odd, I thought we weren't in direct sunlight._

After lifting his head up slightly, Shinji was able to figure out what had happened.

After they had finished lunch, they had gone and lain down together in the shadow of a tree. Shinji had intended for them to lay next to one another, maybe holding hands, but he had been surprised yet again when Rei had curled up right next to him and laid her head on his chest.

Not about to refuse, Shinji had wrapped an arm around Rei and allowed himself to get comfortable. In the warm climate, shaded by the tree, they had both quickly fallen asleep. Now, at least according to the position of the sun, it was late afternoon, and the tree's shade had moved, exposing the two to sunlight.

Shinji knew they would have to move, especially since Rei's pale skin would probably sunburn easily, but he allowed himself to enjoy the closeness with his girlfriend a moment longer.

_Wait, is she my girlfriend? What is 'this' called? We're just fourteen after all…._

* * *

After Shinji woke Rei up, the pair wandered around the park for a while, Shinji being pulled along by Rei as she enjoyed her freedom to chose where they went. Soon, they stumbled across another pair of teenagers going for a walk.

"Hello," the girl said cheerily as she waved, while the boy held out a hand to shake Shinji's, who warily accepted.

"Hey," Shinji said as concern filled his mind. "I haven't seen you guys at school before…."

"Ah, we live on the far side of Tokyo-3," the boy said. "Both of us have parents who are some of the few who are refusing to leave, since they live in the old part of the city that used to be Gotemba. We just came over here to enjoy a nice walk together. There aren't any parks left in our part of the city. All destroyed in the monster battles."

"Hush babe," the girl whispered. "Don't talk about that stuff right now, we're having a perfectly nice day, no need to bring up monsters."

"Ah, my bad. So, what are your names?"

"Oh!" Shinji said, realizing the other couple clearly had no idea that Rei and Shinji were Eva pilots. "Well, I'm Shinji, and this is Rei, my…." Shinji faltered for a second, not sure what to refer to Rei as.

"Girlfriend," Rei suddenly said, as she gave a polite wave to the other couple. Shinji smiled and gave Rei's hand a slight squeeze. "Yeah, this is my girlfriend."

* * *

After parting ways with the other couple, Rei and Shinji began to make their way home, since the day was quickly turning to night. As they neared the building where their apartments were, Shinji began to have some anxieties. "Rei," Shinji asked when they started climbing the stairs to the level their apartments were on. "When you said you were my girlfriend, back there, did you mean, well…."

"We kissed, did we not?" Rei stated bluntly.

"Well, yeah…." Shinji responded slowly.

"Then that means we are dating, and thus, you are my boyfriend." Rei made it sound like the most obvious thing in the world.

Shinji still seemed a little confused, so Rei decided to clarify things for him. She stopped him in the stairwell and pressed another small peck to his lips, surprising Shinji yet again.

"I think of you as my boyfriend. Do you not think of me as your girlfriend?"

"No, of course I do!" Shinji said vehemently. "Then there is no confusion," Rei said as she turned and continued walking up the stairs, clearly satisfied with his answer. Shinji stood still for a second before hurrying after her.

When they reached Rei's apartment, she suddenly turned to Shinji. "I have something for you." She unlocked her door and entered, pulling him along with her.

After shutting the door, she made him sit down on her couch while she went to grab something from her room. Confused, he stroked Mari's fur as he waited for Rei to return.

When she did, he stood up in shock, not believing what she was carrying. "Rei," he softly said.

"It is Christmas after all, so I got you a cello." Rei sat it down while Shinji remembered that it was, in fact, December 25th.

"I remember, before…." Rei turned to Shinji with a solemn expression.

"Before Godzilla took you. You said that you used to play the cello."

Rei approached Shinji slowly as he stood frozen in shock. "I did not understand at the time why I felt the urge to. You were gone. I did not know if you would ever return."

Rei reached out and brushed a hand against Shinji's face. Moonlight streamed in the open window, softly illuminating their faces. She continued speaking, slowly. "I know now why I did. It makes no logical sense. But…."

Shinji felt his breath catch in his throat as Rei struggled with her words.

"But I always knew you would return. You had to return. Because I..." Rei couldn't say it.

"Shinji, I..." she tried again, finding herself unable to speak the words she desperately wanted to say. Years of emotional neglect held her back. She stared desperately into Shinji's eyes, hoping he would understand, when he suddenly said aloud what she was thinking.

"I love you."

Rei's eyes widened. She opened her mouth, but no words came out. Tears pooled in the corners of her eyes as a wave of feelings she never imagined she'd feel suddenly hit her all at once.

"You….love me?" Rei managed to say, her voice filled with hope.

"Yes," Shinji said, a smile growing across his face. "How could I not?"

"But….I'm just me," Rei said with a hint of despair. Shinji wrapped his arms around her and pressed his forehead against hers. He took a deep breath and opened his heart.

"Just you? Rei….you're everything to me."

Right at that moment, on a night with a full moon shining brightly in the sky, while Mari slept quietly, Shinji's earnest words reached Rei, and she finally realized something.

She was loved.

"Shinji….I love you."

**Notes for the Chapter:**

> This has probably been my favorite chapter to write, for obvious reasons:)
> 
> I've always figured that if Rei got a chance to develop more as a person, her sense of humor would end up being very dry, so I ran with that. I also reused the title Moonlight from chapter 9 of A God Incarnate, since its basically a symbol for Rei and Shinji's relationship in this story.
> 
> This chapter is easily the fluffiest I've done yet, but I tried to mix in some good character moments as well. It also marks the halfway point in the entire Evangelion X Godzilla story, and Rei and Shinji getting together was intentionally mapped out to happen at this point. Those who know anything about story structure though will probably guess that some stuff is about to go down, especially considering a certain three-headed dragon is about to arrive. I figured that Rei and Shinji needed a chapter to spend together with no real distractions, and no end-of-the-world talk. Just two fourteen-year-olds awkwardly, but earnestly, expressing their feelings for each other and spending a day together.
> 
> I hope this left everyone satisfied, and I'd love to hear your thoughts. Until next time!
> 
> -AlphaBeta17 (4/10/20)


	7. Terminal Dogma

**December 31st, 2015**

Asuka strolled up to the security guard at the front gate of Nerv with a broad grin plastered on her face. "Hello there," she called out in greeting.

The security guard tiredly waved at the sight of the red-head. "Asuka. You are no longer an employee of Nerv. Why are you here?"

Asuka grinned up at him. "I left some things in my locker, and nobody will let me go get them! I'll be quick, and I won't cause any trouble, I swear!"

The guard knew he should stand strong, but as he was one of the few Nerv employees assigned to work on New Year's Eve, he was feeling a bit rebellious. What's more, Asuka's fiery temper was well known among the staff of Nerv, and he wasn't in the mood to put up a fight.

"Whatever, just be quick about it," he said with a bored expression. Asuka's eyes lit up as he stood aside to let her pass. "Oh, thank you, sir!"

As Asuka walked past the guard, she smirked to herself. _This will be easier than I thought! What an idiot!_

The guard watched Asuka disappear with a bored expression. Just as he was turning around, the thought crossed his mind that maybe he shouldn't have let her in since Misato was still there, but he shrugged to himself. Nerv was big, and so long as Asuka stuck to her word and only went to get her stuff, she shouldn't run into Misato.

* * *

As Shinji drew his bow across the strings of the cello, Rei watched in fascination. The melancholic notes filled her small apartment with a sense of passion that she had never imagined was possible until then. She particularly paid attention to Shinji's face as he lost himself in the music he was playing, his expression one of absolute contentment as he rediscovered his passion.

It sent chills down her spine.

"You OK?" Shinji asked suddenly, his playing coming to a halt as he stared at Rei curiously.

Rei realized that her mouth had been hanging open while she watched Shinji play, and she slowly closed it. "Yes Shinji, I am fine. I just like watching you play."

Shinji looked down at the ground as he blushed. "I'm glad that you do."

He resumed playing, and Rei allowed herself to become lost in her boyfriend's music once again.

* * *

Asuka swung the maintenance door open and was greeted with Gendo's signature scowl. He walked right past Asuka with Ritsuko trailing behind him while Ryoji brought up the rear.

"Hey Asuka, thanks for coming through for us!"

"No problem, it was…." Asuka's voice trailed off at the sight of a pistol in Ryoji's hand. She glanced at Gendo and Ritsuko and noticed that they both had guns holstered on their belts. She gave Ryoji a confused look.

Throwing back his head and chucking, Ryoji held up his hands to reassure the girl. "Oh, don't worry about this, this is just for show."

"Oh! Oh yeah, of course!" Asuka laughed, trying to mask her sudden sense of uneasiness. She hadn't been aware that there would be guns involved.

* * *

Misato stared at the monitors of Central Dogma as she kept watch on the approaching object from space. It's current trajectory placed it crashing down in the Pacific within a couple of hours, assuming it didn't completely burn up on reentry of course.

The UN had chosen not to inform the general public about the incoming object, largely to avoid mass panic. After all, the official story of the Second Impact was that a meteorite struck and vaporized Antarctica, meaning that it wasn't too much of a stretch for officials to assume that the public would freak out about an object moving at an incredibly fast speed towards Earth.

UN astronomers were fairly sure that the object would just burn up on reentry, so there was no need to worry anyway.

That didn't stop Misato from worrying, however. Gendo's words had struck with her, and so here she was, watching the Nerv feeds while almost everyone else was out enjoying New Year's Eve festivities. Even in Tokyo-3, the few remaining people weren't about to skip out on an opportunity to get wasted.

Misato sat up at a sound from nearby. She instantly recognized it as Asuka's voice, and it was rapidly drawing near.

"I can't wait to pilot again! It'll be so much-" Asuka rounded the corner and entered Central Dogma, halting in shock at the sight of Misato.

"Misato? What the hell are you doing here?!" Asuka cried. She suddenly found herself thrown to the side as Gendo aimed a gun straight at Misato.

"Wait-" Asuka yelled.

BANG!

Asuka shrieked at the sound of the gunshot and threw herself to the ground. She looked up and breathed a sigh of relief. Misato had dove to the side and hidden underneath one of the desks, the bullet embedding itself in the chair she had just been sitting in.

"Misato! You weren't supposed to be here!" Gendo's voice rang out while Misato scrambled on the underside of the desk for the compartment where a small pistol was stashed.

"I see you convinced Asuka to let you in. Can't say I'm surprised, but you really should've picked a brighter person to get you in here!" Misato called out as she cocked the gun and prepared to fire at Gendo, who was cautiously keeping an eye on the desk Misato was hiding under.

"Misato." It was Ritsuko's voice. She coldly made an appeal to her old friend. "Come out with your hands above your head. There's three of us, and you are no match for us all."

Misato narrowed her eyes. "You are mistaken," she said dangerously, before jumping out from underneath the desk and firing several shots at Gendo, who ducked down just in time to avoid them. "Bitch," he snarled out, before motioning for Ritsuko to circle around to cut off the other exit point to Central Dogma.

"Wait!" Ryoji said. Ritsuko halted and turned on him with a furious expression. Ryoji ignored her harsh glare. "Misato, we don't want to hurt you. Please, come with us quietly."

"Ryoji," Gendo quietly said. "Now isn't the time for this."

"No, this is the time," Ryoji said. "I haven't been fully honest with you, Gendo. You see, I'm helping you because-"

BANG!

Asuka gasped in horror as Ryoji slumped to the ground clutching his shoulder where Gendo had shot him. "MR. KAJI!" Asuka screamed.

Misato's eyes widened in shock. "No…."

BANG!

Ritsuko had taken the opportunity to catch Misato off guard, firing her gun at point-blank range directly into Misato's gun-wielding hand. Misato yelled in pain and dropped her gun, which Ritsuko quickly picked up and holstered.

Ritsuko sighed. "Honestly, what a shame."

As Gendo walked past Ryoji, who was now curled up in a fetal position, he couldn't keep the disdain out of his voice. "Ah, Ryoji, my fine young lad. You served your purpose well, but frankly, I don't give a damn what your motivation for helping us was."

Gendo grabbed Misato by her hair and started dragging her with him. She writhed under his grasp and let out a yell of pain when her hand that had just been shot was cruelly grabbed by Ritsuko, who managed to look slightly contrite at the sound of her former friend's screaming.

"Come, Misato. You as well, Asuka. There are things I'd like to explain. An audience might as well appreciate what has been accomplished, in case we're all about to die."

Nobody noticed as Ryoji pulled out a transmitter and pressed a button on it.

* * *

Misato found herself on her knees in an elevator with a gun held to her head by Ritsuko while Asuka stood nervously beside her. Gendo was facing away, seemingly drilling holes into the walls with his eyes while the elevator descended into the dark depths beneath Nerv.

"Where are you taking us?" Misato managed to groan out while she tried to stop the blood dripping from her hand.

"To Terminal Dogma," Gendo responded. "I trust none of you were able to breach it in my absence?"

"Unfortunately, you are correct," Misato said. "Ritsuko's firewalls were impossible for us to break through."

"As they should be," Ritsuko huffed. "I didn't spend my whole life in my mother's shadow for nothing."

"Ha!" Misato snorted. "Your mother. You told me all about her. How she viewed you more as a successor than a daughter. You and I would get drunk and you would tell me all about how terrible growing up with her was."

Ritsuko looked away as Misato tried to get to her feet, only to be shoved back to the ground by Gendo.

"Still under Gendo's thumb, I see," Misato chuckled. "Why the hell did you ever start listening to this maniac anyway? We both know he's crazy!"

"He's not crazy," Ritsuko murmured to herself. It sounded more like she was talking to herself.

"What the hell is going on?!" Asuka suddenly yelled. "You….you shot Mr. Kaji!" Asuka stared daggers at Gendo's back as she spat out her words, laced with venom. Tears started to stream down her cheeks. "This wasn't in the plan!"

Gendo suddenly rounded on Asuka as his facade broke, revealing his impatience with the teenage girl. "Damn you! And I thought Shinji was an idiot. Did you honestly believe everything we told you? Did you never stop to question it?"

Asuka looked down at the ground miserably while Gendo scoffed. "Of course not. You like to think of yourself as a brilliant, gifted youngster, but you're no more special than any other child. The only reason you're even an Eva pilot is because your father cheated on your disabled mother, and she killed herself. A stroke of luck, if you ask me, since her ability to help develop the Evas had reached its limit. We needed a child born after the Second Impact with a recently deceased mother, and you fit the bill."

Asuka felt her soul crumble as Gendo leered over her, reaching out to cup her chin while Ritsuko averted her eyes, looking almost regretful. "It's ironic, really. Your mother spent several years working on the Evas. She was the one who figured out that a mother's soul was the key, but she never suspected that she would be subjected to her own ideas."

Asuka slid to the floor as reality hit her. "My mother….is in my Eva?"

Misato gasped in horror. "No. You bastard. You have to be lying, the same as with Shinji and his mother. There's no way…."

The elevator suddenly slid to a stop, and the door flew open, revealing a dark hallway lit only by a single lightbulb. At the end was a state-of-the-art security door with a passcode panel on it. Ritsuko kicked Misato in the back, forcing her to her feet as Gendo grabbed Asuka's arm and pulled her along with him.

"Believe it," Ritsuko sneered, all traces of her momentary regret vanishing. "Both Asuka and Shinji's mothers are trapped within their children's respective Evas. Now, we will show you how we did it."

* * *

Ghidorah cracked open his eyes as he sensed the approaching planet. With a wide yawn, he spread his massive wings as he continued to slow down. He had been instinctively slowing his approach for the past several months, and now, he was only half an hour away from reaching his next planet. Earth.

Cracking his joints, he began to reach out with his powers to sense the size of the planet, and its condition. Surprisingly, it wasn't in that bad of a shape. Another quick scan confirmed why.

It was relatively small, the same as the rest of this solar system. Only a few objects large enough to be considered planets, and a sun still young, only four billion years old. With Ghidorah's organic beacons, the larger the planet, the greater the force behind its destruction.

No matter. This would be a quick planetary destruction, no doubt. Assuming, of course, that there weren't any surprises.

* * *

Misato stared in horror as Gendo and Ritsuko led her and Asuka through the years of development in Terminal Dogma, exposing her to the many inhuman sins of science committed by Gendo, Ritsuko, Ritsuko's mother, Asuka's mother….and Shinji's mother.

"And this is where we assimilated Yui into the Core of Eva-01. She insisted, after all," Ritsuko said. "She was a lot braver than Asuka's mother."

A dark thought hit Misato. While a part of her didn't want to know the answer, the other, more pragmatic side, knew that it would be better to know as much as possible. "Ritsuko," Misato said slowly. "Who is inside Rei's Eva?"

Ritsuko stopped dead in her tracks. After letting out a loud sigh, she turned to face Misato. Her expression took on a haunted note for a second, before being replaced with grim arrogance.

"Naoko Akagi. My mother."

Misato's eyes widened. She tried to say something, but couldn't bring herself to speak.

"My mother," Ritsuko continued, "was brilliant. The lead architect behind the Evangelions, she began an affair with Gendo over there, not long after Yui sacrificed herself to give life to Eva-01. Of course, it was all a part of Gendo's plan to manipulate my mother into killing herself."

Ritsuko's eyes glazed over as she continued with her haunting story, while Asuka crept over to Misato, clutching at her uninjured hand. For a brief second, Misato considered pushing Asuka away.

_No. Asuka and I will need each other to get through this._

"Gendo began sleeping with me as well. I was so lucky he chose me to be his mate. You know, the bridge technicians think they're so smart, having figured out that Gendo and I were a thing two years ago. Ironically, we've actually been together for years. When my mother found out, she killed herself out of anguish. Happiest day of my life, seeing my mother's dead body being absorbed into a monster for that blue-haired bitch Rei to pilot. Speaking of which…."

Ritsuko stepped up to a control panel and punched in a code. A panel on a nearby wall slid open, revealing a vat of green liquid. Asuka screamed at what lay within, while Gendo chuckled at the sight.

Multiple floating clones of Rei Ayanami.

Misato stared in horror, unable to speak at the revolting sight. Suddenly, every single of the Rei clones opened their eyes, revealing the same red iris color that the Rei known to Misato possessed. Misato was barely able to stifle her scream, while Asuka passed out in shock.

"God help us!" Misato screamed. She collapsed to the floor and wrapped her arms around Asuka, the animosity between the two long forgotten.

* * *

Rei's eyes shot open.

_That was a strange dream._

After Shinji had finished playing his cello for the night and started getting up to head back to his apartment, Rei had grabbed his arm and led him to her couch, where she 'made' him sit down so she could rest her head on his shoulder.

It hadn't taken long for sleep to overtake her, and now it appeared that Shinji was fast asleep, apparently having accepted the situation he was in.

Rei glanced down to find Mari curled up on her lap. The black cat cracked open its one good eye and lazily stared at Rei for a moment before closing it again, having confirmed that the sudden movement had just been Rei waking up.

_What was I dreaming about?_

A strange feeling came to Rei. It almost felt like apprehension. After several minutes, she forced herself to relax again, settling back against Shinji.

_It's probably nothing. Besides. Shinji is warm. And comfortable._

Rei closed her eyes.

* * *

Misato stared in confusion as each Rei clone closed its eyes at the same time, creating an odd effect, almost like a puppet was controlling the lifeless bodies.

"How are they doing that?" Misato whispered.

"They are all connected to Rei. The true Rei, if you will," Gendo said casually. "To be honest, there is no such thing as Rei Ayanami. At least not anymore."

"What do you mean?" Misato asked weakly.

_How can this get any more insane?_

"Well," Ritsuko said, "Rei Ayanami was once a normal girl. She looks nothing like how she does today. That is, until we found her and her mother, Moyoko Ayanami, on the streets of Tokyo-3. Starving, and helpless, we took the two of them in, not long before Yui sacrificed herself. It was rather simple, killing the mother, and injecting Rei with some of Yui's genetic code, forcing her body to restructure itself to look exactly like Yui. It didn't work perfectly, of course, hence the red eyes and blue hair."

As Misato collapsed to her knees in shock, Gendo stepped in and continued for Ritsuko. "Yui hoped that if she was ever able to be rescued someday, she would have a fresh, young body to inhabit. One that was identical to the one she sacrificed. We took several homeless girls, all around the age of three, from around Tokyo-3 and created identical clones of Yui out of them. Rei was the first, and we linked all of their bodies together so that as Rei went about her life, these girls here would continually grow as well."

"Rei Ayanami is a vessel for Yui Ikari," Ritsuko said. "Assuming, of course, that Yui can be rescued."

The implication of this wasn't lost on Misato. _Ritsuko doesn't believe Yui will be rescued, which explains why she went along with everything. Gendo manipulated her, just as he manipulated Naoko. God, this is crazy. He's crazy._

_Wait, so this means that Rei looks exactly like Yui Ikari._

_Oh no. Shinji…._

Gendo could tell Misato had just figured it out. He couldn't help but smirk. "Like father, like son, I suppose."

"But why. Why do all of this? And what if Rei died in battle? Why use one of your precious Yui clones as an Eva pilot?"

Gendo stared at Misato for a second before laughing. "The real question is why not. We needed the first of the 'Yui clones' as you so crudely called them to grow, and I figured that I could put it to work."

Gendo suddenly frowned. "And, please. Don't denigrate my wife by calling these things her clones. They are not her clones, they are worthless children that I have taken to be used for a greater purpose. They are Yui in physical build alone."

Misato saw an opening and took it. _Maybe I can turn Ritsuko against Gendo._

"So if you save Yui, you'll essentially kill Rei and give her body to Yui? And then what? You'll fuck it? And what about Ritsuko?"

Ritsuko lashed out and punched Misato, raw anger etched in her features. "Shut up! Yui will not be rescued! I will be with Gendo, forever! You hear me?! I WILL BE WITH GENDO FOREVER!"

Misato rubbed her jaw as she stared at her former friend. "Ritsu. Gendo has you under his thumb. Can't you see that he's using you? Break free, goddammit!"

"SHUT UP!" Ritsuko screamed as she started beating Misato. Gendo chuckled, watching as the once proud and independent scientist attacked her friend.

"Don't you see, Misato? Your friend is mine. She's been mine for a long time now."

* * *

Ghidorah could see the planet. Blue and green all over, it looked rather peaceful, even in the aftermath of his organic beacon explosion fifteen years before.

Time to shatter what peace was left.

Ghidorah roared with each of his three heads as he entered Earth's atmosphere.

**Notes for the Chapter:**

> In case you are unaware, unfortunately, the fourth Evangelion Rebuild film has been postponed due to the ongoing coronavirus outbreak. It is unknown when it will be released now. However, they did release the official English title for it, as well as a tagline.
> 
> Title: 'Evangelion: 3.0 + 1.0 Thrice Upon a Time'
> 
> Tagline: Bye-bye, all of EVANGELION.
> 
> Thrice Upon a Time? And a poster featuring Shinji walking towards a railway junction? Rather interesting if you ask me. Seems choice will be a big part of the story. Hopefully, we won't have to wait too long for this movie.
> 
> Meanwhile, Ghidorah is here! I also changed up Rei's backstory a bit. In writing this story, my goal is to create something new, not just tell Evangelion with Godzilla thrown in, and through lore changes like this, as well as unique conflicts that weren't faced in canon, I hope I've accomplished that so far. Also, yes, I got the name Moyoko from Hideaki Anno's wife's name.
> 
> Until next time, reviews are always appreciated!
> 
> -AlphaBeta17 (4/17/20)


	8. Ghidorah's Arrival

**December 31st, 2015**

Despite the immense heat generated as he descended through the Earth's atmosphere, Ghidorah was perfectly comfortable, his golden scales easily withstanding the heat and pressure.

Loud booms echoed across the Pacific, and the night sky began to glow a harsh orange as flames licked off Ghidorah's wings and descended upon the world below. Ghidorah could sense small mechanical objects already on their way to intercept him. While Ghidorah didn't know that they were called jets, or that they came from Hawaii, he knew that they were of no concern.

Tucking his wings around his body, Ghidorah braced for impact against the ocean surface below.

* * *

"Ritsuko, make sure Miss Katsuragi is unable to move," Gendo commanded. "It'd be a pity for her to do something irrational and force us to kill her."

Ritsuko nodded wordlessly as she wiped Misato's blood off her hands and stood up. In front of her, Misato lay tied up with her arms behind her back. Her face was bruised from repeated kicks, and her leg was twisted at an odd angle.

"How," Misato mumbled aloud. She looked at Gendo with an air of hopelessness. "How did you do this to my friend?'

Gendo walked over to Misato and knelt down next to her. "Ritsuko," he called out. "Tie up Asuka as well. I don't want her to be able to cause any trouble when she eventually wakes up."

While Ritsuko set about her task, Gendo leaned over Misato and spoke quietly into her ear.

"You have no idea how easy it is to worm your way into people's hearts. To slowly, over time, become the very reason they continue to exist. If you have the intelligence, and the will, you can control anyone you desire. You can make them believe that nobody else matters, and that nobody else will ever love them. They then turn to you, and give everything they have. I wouldn't expect someone like you to understand. The only one who ever did was Yui. She was my equal in every regard, which is why it's a pity my son ended up being such a disappointment. Even as a toddler, it was obvious. Weak-willed and pathetic, he is exemplary of everything I look down upon in humanity. Hopefully, in my absence, he has changed, and become far stronger."

A loud blaring alarm suddenly went off. Gendo looked up with an air of dread.

"It has arrived," he whispered to himself. "That means it's already punching through the layers of the atmosphere and not burning up. I was right."

It slowly dawned on Gendo. "I was right all along. It's here to destroy us." With a look of urgency on his face, he leaned over Misato and spoke with renewed vigor. "Is Shinji strong enough to face it?"

Misato couldn't even look Gendo in the eyes. "I don't know. You certainly didn't help matters."

"At least I tried," Gendo scoffed. "Ryoji's ORCA device worked wonders for attracting monsters for our pilots to battle. Hopefully, the practice was enough to prepare him."

"Practice?!" Misato barked out a humorless laugh. "You're so delusional. Do you even care about all the people that died in all those attacks?"

"I care about the bigger picture." Gendo turned to Misato, and for a brief second, he looked contrite. "If I could prepare Shinji to battle this threat, if he can save us all, save the world in fact, then the lives sacrificed were all worth it. What's more important. A single city, or humanity? You tell me. Now, we stand a chance. He might pull this off."

Gendo turned back to the monitors. "Or he might not. If that's the case, then at least we're down here. Even if whatever this is ends up destroying the world above, we will survive below it. Maybe it will be beneficial. Maybe the weakest will be killed, and the strongest, like me, will be able to band together and build a new world. A better world."

Gendo's brow furrowed in anger. "If everything had gone according to my plan, we wouldn't be betting everything on Shinji controlling Godzilla anyway. Yui would be in control of it, and with her intelligence, she'd save us all."

"Congratulations," Misato spat out. "Your inability to be transparent has screwed us all. Your cruelty stunted Shinji's growth as a pilot. If you'd believed in your own son from the start, if you'd even tried to care for him, maybe we'd be better off now!"

"Maybe," Gendo said. "Or maybe not. I took a calculated risk. Now, assuming he makes it to Godzilla, we will find out if he's ready."

Gendo slowly turned to Misato. "But he doesn't know. From what I hear, you never told him about this threat. He thinks tonight is just like any other night, and for all we know, he'll die long before he can get to Godzilla."

"I had no choice!" Misato yelled, panic setting in as she realized her mistake in hiding the truth. "If I told him about this incoming threat, he'd have cracked under the pressure! Besides, how could we have known it would make it through the atmosphere?!"

Gendo shook his head. "You should have anticipated multiple outcomes and been better prepared. Pathetic. What a great Commander of Nerv you made. From what I've heard, you were cold and heartless. Did you beat him? Did you beat my son?"

Misato froze. "No. I, I didn't…."

Gendo scoffed. "Don't try to deny it. I can't blame you. He's recalcitrant nature invites harsh discipline. He has only himself to blame."

Misato shook her head. "I was wrong. I should never have done that to him."

"That there proves why you are ineffective," Gendo said. "You lack the will to do what is necessary. Now, it is time to see if we shall all pay the price."

* * *

Shinji bolted upright at the image of a three-headed dragon bearing down on him.

_What? Where am I?_

After a moment, Shinji relaxed a bit. He was sitting on Rei's couch in her apartment. She was asleep next to him with her head on his shoulder, with Mari on her lap.

_It was just a dream. That's all it is._

A loud siren pierced the air of Tokyo-3. Rei's eyes shot open and she sat up quickly. After listening for a moment, her expression became grim.

"That is not the same siren used for monster attacks," she stated intently. "This is the one used for natural disasters."

* * *

Ghidorah slammed into the ocean surface with a massive sonic boom. His huge size created an impact upon the surface of the water so large that a wave 10 meters high was created.

It would travel across the ocean, becoming a massive tsunami that would destroy cities worldwide, and end the lives of millions.

Ghidorah knew all of this for a fact. He'd long ago figured out that impacting into oceans instead of on land was a surefire way to devastate worlds quickly and efficiently.

He burst triumphantly out of the ocean with a roar from all three of his heads. He had arrived on a new planet, and it was just waiting for destruction. All he had to do was-

Ghidorah suddenly froze. While he hovered in midair with massive flaps of his wings, he looked to the west in confusion. Was that what he thought it was? No, of course not. There was no way.

He figured he was going crazy. He could sense a creature with raw power that rivaled his own. While he had come across creatures like that plenty of times, it was never like this.

The more Ghidorah reached out with his senses, the more unsettled he became. Whatever this being was, it was an unholy amalgamation of two different, monstrous creatures. A being-that-was-two-beings. Both vying for control, but one clearly in charge. For the moment.

One of the creatures seemed to be a deformed, ancient animal that had been artificially raised to the level of a god. Even from several hundred miles away, Ghidorah could feel the rage emanating from it. It wanted one thing, and one thing only. Revenge on the beings of this world for making it what it was, and it would do anything to achieve it.

But the other creature was even more baffling to Ghidorah. It was made from thousands of individual, intelligent beings who were forcibly made into one, singular creation that now held the soul of one individual.

An attempt by mortals to create their own immortal being. A god of their own.

It disgusted Ghidorah. It reminded him of his own creators. This was a creature engineered for the purpose of destruction. What's more, there seemed to be three of them. In addition to the one that seemed to hold dominion over the deformed god-like animal, there were two other ones that stood freely.

Ghidorah did not know what these things were. But he sensed that if he wanted to destroy this world, he would have to face them. Specifically, he would have to face the being-that-was-two-beings.

With one single massive wing flap, Ghidorah propelled himself forward at several hundred miles per hour. He was heading west to confront this monstrosity.

* * *

Clutching Mari's cat carrier against his chest with one arm, Shinji ran with his other hand held firmly in Rei's. The loud emergency siren filled the air with a resounding sense of dread.

It felt like the world was ending.

Everyone in Tokyo-3 had heard the sonic booms, but almost nobody knew what it was. Shinji had tried contacting Misato, who he knew was at Nerv, but to no avail. Meanwhile, citizens were panicking. At first, the wisest choice had seemed to be to shelter in place.

Then the news came over the emergency sirens that something massive had broken through the atmosphere and smashed into the Pacific, creating a huge tsunami that was now heading for the coast of Japan.

While Rei had wanted to stay put, Shinji had convinced her that they should try getting to higher ground. There was no telling how devastating the tsunami would be, and Shinji didn't want to be in the city to find out.

Now, the two teens, along with Mari, were heading towards Mt. Fuji next to Tokyo-3. Shinji figured that it was the safest bet right now, and he was taking it.

As they ran through the outskirts of Tokyo-3, they were soon joined by others. It appeared that everyone had the same idea to get to Mt. Fuji.

Shinji and Rei were at an advantage, already living on the side of town closest to Mt. Fuji. Many others who lived closer to the coast would have to either go around the destroyed center of Tokyo-3, or risk cutting through and being exposed to the radiation left over from Godzilla's attack.

Godzilla itself still lay motionless next to Nerv. While Shinji had considered trying to make it to Nerv, the notion of being forced to get back inside the Godzilla/Eva-01 hybrid was too much for him to handle. It would be better to just try to survive the incoming disaster the normal way.

"Shinji," Rei suddenly said, her breath still relatively even despite the nonstop running.

"Yeah?" Shinji breathlessly responded.

"How long are you going to hold Mari?"

"What?" Shinji came to a stop and gasped for air. Mari wasn't fully grown, but she still weighed about six pounds, which was enough to wear Shinji down after running for so long, especially carrying her in a cat carrier.

"I can't put her down," Shinji said desperately. "I can't just leave her!"

"No," Rei said gently. "I will carry her for a while. You're getting tired."

Shinji blinked. Rei was right, he was tired. After a moment, he softly smiled at her.

"Here," he said, handing Mari's carrier over to Rei, who gave Shinji a quick smile.

"We should keep moving," she said as she turned to keep running.

"Wait," Shinji suddenly called out. Rei turned around and was surprised when Shinji pressed a quick kiss to her lips.

"Thanks," he said softly. "Now, let's keep moving."

Rei blushed, and the two continued on.

* * *

Ryoji gasped for air as he tried to stop the flow of blood pouring out of his bullet wound.

A crackle suddenly came from his transmitter. "Come in, come in Kaji. Where are you? What the hell is going on?"

"I'm here," he growled out. "I've been shot, I need help immediately."

"You're at Nerv, right? How did the infiltration scheme with Ikari go?"

Ryoji rolled his eyes as pain spiked through him. "Considering I've been shot, I'd say it went well," he managed to get out. "Does anybody know where Shinji is? I'd say now is a damn good time to reveal ourselves."

"Negative, we stopped by Misato's apartment. Rei's as well. Neither were there. Nobody knows where they are."

"Shit," Ryoji groaned. "The dragon's coming, right? Along with the tsunami?"

"Yes, the tsunami is gonna strike Tokyo-3 any minute now. The dragon isn't far behind, just like we predicted. It's all going as the Prophecies said."

Ryoji sighed as he thought back on how he had gotten to this point. Nerv had uncovered ancient documents on Infant Island, back in October before Godzilla's second attack. Ryoji had managed to convince Gendo that they were worthless, and after Godzilla had attacked for the second time, Ryoji had managed to secretly swipe them in the confusion. While Gendo and Ritsuko had been running around locking down Ritsuko's labs, Ryoji had snuck into Nerv's archives and stolen them right under everyone's noses. He had given them to the organization he was truly loyal to, and they had managed to translate them.

So far, everything predicted had come to pass. If things continued to come true….

Ryoji shivered as another spasm of pain racked his body.

What was about to take place was nothing short of a biblical-style legend.

* * *

From their vantage point on the slopes of Mt. Fuji, Rei and Shinji watched as the tsunami slammed into Tokyo-3, tearing through and utterly destroying it. While the people near them variously collapsed to the ground and wept for the thousands still in the city, others screamed at the notion of the millions across the world that were dying right now. Not every major city had a convenient mountain sitting right next to it.

To Shinji and Rei, that all seemed so irrelevant. All they knew was that they had survived.

They watched as they saw the area of the city where they had lived was engulfed in waves. They watched as the pyramid of Nerv was battered, with only the top half sticking out above the water. They watched as the motionless monster, Godzilla, was knocked over by the force of the tsunami.

Shinji and Rei wondered if Misato was safe at Nerv. If the bridge crew had managed to get out of the city in time.

What would become of them now?

A roar, coming from the Pacific, answered that question for them.

Shinji felt his heart stop when a being appeared out of the night sky and descended on Tokyo-3. He had seen this three-headed being before.

Ghidorah had arrived in Tokyo-3.

**Notes for the Chapter:**

> I have just posted the first chapter of a new story I'm going to be working on, an Attack on Titan/Godzilla crossover. If you enjoy this story, I'd appreciate it if you would consider checking that other one out as well. I'm very excited to get started on it, as I've been planning it for a while now.
> 
> It won't interfere with this story, don't worry. I'll still be uploading a new chapter every Friday night, while also uploading chapters of that new story weekly, starting this Tuesday night.
> 
> Until then, reviews are always appreciated!
> 
> -AlphaBeta17 (4/24/20)


	9. The Wrath of Ghidorah

**December 31st, 2015**

Ghidorah scanned Tokyo-3 as he flew overhead, searching for the being-that-was-two-beings. He narrowed his eyes when he spotted it lying face down in the mud left behind by the receding tsunami. With a hostile roar, he slammed into the ground next to it, landing on his feet and spreading his wings for maximum intimidation.

Godzilla didn't respond.

Ghidorah cocked his center head in confusion while his right and left heads leaned down to examine the being-that-was-two-beings. Sniffing at its motionless body, he couldn't help but feel a surge of disappointment. He had been looking forward to a fight.

With a roar of anger, he struck with all three of his heads like a viper, his teeth easily breaking Godzilla's skin. He injected electricity directly into Godzilla, hoping to jolt it awake.

Godzilla's eyes snapped open as it suddenly became aware of its situation. The electricity racked its body with pain, snapping between the points where the metal armor of the Eva was jutting out.

Godzilla tried to roar, but found something mentally blocking him. It was another being that was inside of him, no, controlling him.

Evangelion Unit-01.

Godzilla tried again, only to find himself pushed back into his subconscious as the Eva shook off the momentary shock from Ghidorah's electricity and re-exerted its control over him.

Ghidorah could sense the turmoil engulfing Godzilla's body. For a brief moment, it was like the creature imprisoned in its own body had reared its ugly head, only to be shoved back down.

It enraged Ghidorah, seeing what the intelligent beings of this world had done to this creature. Ghidorah was destructive, but he held much respect for other god-like beings, and to see one of them subjected to such torture was infuriating.

With a violent roar that echoed across Tokyo-3, he took off with a massive burst of his wings. When he reached several thousand meters high, he began to fly towards Mt. Fuji.

* * *

Shinji ran with Rei's hand clutched in his own as Ghidorah approached them. They were heading back down the mountain with the panicking masses of Tokyo-3, hoping to avoid whatever was about to happen.

Ghidorah positioned himself above Mt. Fuji and released an ear-piercing cackle as light began to emanate from his body. In a single instant, the light coalesced up through his necks and into his mouths, bursting free in explosive fashion. The three golden beams struck Mt. Fuji and pierced the mountain, spreading like spiderwebs across its upper half.

Shinji and Rei were safe for the moment, being located on the lower half of the moment, but that safety would be shortlived.

Mt. Fuji began to disintegrate. With Ghidorah's power flowing through it, gravity began to distort, lifting pieces of the mountain from the ground and into the air.

The citizens of Tokyo-3 could only watch in terror as Ghidorah tore the very top off Mt. Fuji and held it in midair, a pulsating, hovering mass of rock and soil that no longer resembled the peak of a mountain.

Shinji stopped running, figuring there was no escape from what was about to happen. He wrapped his arms around Rei and sunk to the ground, hoping that this wouldn't be the end.

With a strangled roar, Ghidorah sent the pieces of Mt. Fuji soaring across the sky, creating what looked vaguely like a meteor shower. He sent the endless barrage of rock barreling towards the west, where it would rain down across eastern Asia, killing millions that hadn't already been wiped out by his tsunami.

Shinji buried his face in Rei's neck as he felt an overwhelming sense of doom envelop him.

A familiar roar echoed across the landscape. Rei looked up in recognition, turning back to face the now decimated upper half of Mt. Fuji.

"That sounded like Anguirus," she said.

"What?"

With the top half of Mt. Fuji now completely gone, the three monsters that Shinji and Rei had battled months before were now suddenly exposed.

Anguirus, Baragon, and Varan. They had taken shelter within Mt. Fuji following their battle with the Evas and entered a state of hibernation.

As the three monsters began to wake up, they were faced with an enormous three-headed dragon hovering overhead.

They clambered to their feet and began to put on a defensive display. Standing side-by-side the three monsters barred their teeth and roared in warning, hoping to prevent their deaths at the hands of this extra-terrestrial invader.

With what could almost be described as a smirk, Ghidorah allowed himself to fall to the ground, landing next to the three monsters. They gave up all pretenses of resistance and simply bowed their heads in fear.

Ghidorah leered over them for a moment before cackling in satisfaction. Raising his heads skyward, he let out a bellowing call that punched through the atmosphere and echoed across the planet.

Monsters around the world began to wake from hibernation, answering Ghidorah's call to destruction. Within minutes, cities worldwide, many of which had already just been devastated by the tsunami, found themselves under attack by monsters.

Ghidorah roared in triumph from atop the devastated Mt. Fuji. In punishment for their crimes, this measly little planet and its intelligent population would not be destroyed immediately.

Instead, prolonged destruction would take place at the hands of an army of monsters, all under his control.

Ghidorah snorted in satisfaction as he took to the air to begin generating a worldwide storm that would add to the chaos. Below him, the monster trio descended on what was left of Tokyo-3.

As a new year began on Planet Earth, Ghidorah took a moment to reflect. He quite liked this newfound status he had attained. In the span of a couple of hours, he had smashed into this planet with enough force to create a devastating tsunami. Then, after discovering the horror that was the being-that-was-two-beings, he had torn off the top of a mountain and sent it flying across the atmosphere. Finally, he had claimed his rightful status as King of the Monsters.

* * *

**January 1st, 2016**

Asuka slowly opened her eyes. Memories of what had been revealed to her came flooding back into her mind, threatening to overwhelm her.

_Mr. Kaji was shot. He's probably dead now._

_Rei has a bunch of clones of her sitting beneath Nerv._

_My mother is inside my Eva._

_My mother is inside my Eva._

Asuka groaned as the reality of the situation hit her.

_My mother is inside my Eva, and it seems like the world's about to end._

"Asuka?" It was Misato's voice.

"No, not you," Asuka mumbled. "You're as bad as me."

Misato sighed. "I suppose you're right. I failed. I failed everyone."

"Got that damn right," Asuka said venomously. She tried to sit up, only to find she was tied up. She began to panic while Misato looked on in shame.

"I'm sorry, Asuka. They tied us both up. I think we're in some kind of storage closet in Terminal Dogma. Ritsuko's been stopping by every few minutes to update me on what's going on up there on the surface. Oh, and at this rate, I'll lose my hand. Not that it matters."

"Ha!" Asuka laughed humorlessly. "Ritsuko shot your hand, that's right. Pretty funny, if you think about it. She was your friend, _was_ being the operative word."

Misato growled. "Asuka, I'm trying to be friendly here. Why the hell do you feel the need to be so toxic? It doesn't endear you to anyone, it just pisses people off."

"Really feeling the friendliness, then," Asuka muttered.

"That's not fair," Misato said tiredly. "And you know it isn't."

Asuka shrugged. "Who cares? You certainly don't."

"Yeah? YEAH?" Misato yelled. "WHY THE HELL WOULD I?"

Asuka stared at Misato in shock. She tried to keep the sudden rush of emotions down, but in the end, she failed.

Misato could only watch, ashamed as Asuka broke down sobbing.

* * *

"Shinji."

Rei's voice sounded tired as she tapped Shinji on the shoulder. He was sitting on a sheltered sidewalk bench while Rei stood directly in front of him, Mari's cat carrier still held at her side.

"Yeah," he responded as he stared at the ground, trying to zone out the destruction coming from Tokyo-3 below them. Overhead, Ghidorah was continuing to generate his massive, worldwide storm. The wind was already sweeping through the air, picking up loose debris and sending it flying.

"I think we should fight."

Shinji's head snapped up as he stared at Rei in raw horror. "No, I can't."

"But we must. We are Evangelion pilots. We are the only ones capable of fighting this creature. If we do not, then we shall eventually perish."

Shinji wanted to agree with her. In fact, he did agree with her. But the resounding fear of getting back into the abomination that was Godzilla overwhelmed him once again.

"Then it looks like…." Shinji swallowed. "Then it looks like we'll die."

"SHINJI!" Rei's shout shocked Shinji to his core. He stared up guiltily as Rei glared him down. After a moment, her gaze softened back to its usual, somewhat blank stare. Of course, it wasn't nearly as blank as it had once been. Compared to when he first met her, it was highly expressive.

"I apologize," she softly stated. "But I need your full attention. I'm….I'm scared. I don't know what we should do."

Rei looked lost as she forged ahead. "I spent my whole life not caring whether I live or die. You were the one who convinced me to live. Not for anyone else, but for myself. And now you say you don't care if you die? I don't understand."

Shinji looked up into her gaze and tried to smile. It came out forced, but his eyes expressed his resounding care. "Rei, you don't need to apologize. I need to apologize. I guess I just…."

Shinji felt lost as he continued. "I don't like myself. I spent my whole life feeling like I don't matter, and when I finally did, it hurt so much. It's easier to convince myself that I don't matter. It makes it easier, because if I do matter, then surely I'm a massive disappointment."

"But you're not a disappointment." Rei's voice was shaking slightly, but it was full of more emotion than she had ever shown. "Not to me."

Shinji stared into Rei's eyes, searching for any sign of dishonesty.

_No. Rei would never lie to me._

Shinji took a deep breath. If they were to get through this, he would have to bare himself to her fully. "It feels like the world's ending around us. Probably because it is. I can't tell you what we should do, because I don't know the answer. Really, I never have. I didn't want to come to Tokyo-3, but I was 'required' to come, so I did. I never wanted to pilot the Eva, but I did, because if I didn't, you would've had to pilot when you were injured. It turned out that you couldn't pilot my Eva, even if my father wanted you to. It was a bluff. But if I hadn't gone ahead and piloted the damn thing, then Godzilla could have killed many more people, way back in his first attack, all those months ago."

Shinji stopped as he looked out across the destroyed Tokyo-3.

"A lot of those people are probably dead now anyway. But maybe….maybe that doesn't matter. We're just kids, after all. How can anyone expect us to take responsibility for the lives of millions?"

Shinji didn't know where he was going with this ramble, but he didn't stop.

"It's not fair. But life isn't fair. This is how it is. I've been telling myself not to run away ever since I got here. Maybe I should run away. But today, I won't. I'm not going to run away."

"I'm not going to run away."

Shinji narrowed his eyes.

"I'm _not_ going to run away. _We're_ not going to run away. We're going to go back to Nerv, and we're going to do our jobs. Maybe we'll fail. Maybe we'll die. But if we don't try, then we're dead anyway."

Shinji shrugged helplessly as his speech came to an end. "If we're going to die, then we might as well die fighting for each other."

Shinji felt his throat start to burn as it hit him.

_We're going to die. We're going to fight this dragon, and we're probably going to die._

Tears began to fall as Shinji put his head in his hands and began to weep in front of Rei.

For a moment, he became hyper-aware of everything.

Rei was standing in front of him, motionless. Mari was in a cat carrier, held at Rei's side.

Tokyo-3 was in ruins.

A storm was swirling in the sky.

The air stank of smoke and upturned soil.

In the distance, sounds of destruction and thunder echoed.

Someone was sniffling. But it wasn't Shinji.

_Wait. Who's crying?_

Shinji looked up to find Rei in tears. She looked lost, and confused. She sank to her knees in front of Shinji.

He immediately abandoned his place on the bench and sat next to her. He wrapped his arms around her and clutched her body to him.

He could feel the quiet, but rapid beats of her heart.

_She's as scared as I am._

"I'm sorry," he said quietly. "I-"

"No. Don't be."

Shinji was about to keep talking, but something inside him told him to be quiet and just embrace this moment while it lasted.

So, that's what he did.

* * *

Shinji and Rei faced the giant steel pyramid of Nerv. The damage from the tsunami from just a few hours before was chillingly apparent, with the entire lower half of the pyramid being in a state of disrepair that would take years of normal weathering to reach.

Rei glanced at Shinji by her side. "Are you ready?"

"No. Let's go."

As the two walked up to the base of the pyramid, they suddenly heard a shout.

"Shinji! Rei! Is that you?!"

They turned, and were startled to find Makoto running up to them, Miki and Daisuke close behind him.

"Guys! You're alive!" Shinji said in surprise.

Miki scoffed. "Oh please. It'll take more than the end of the world to kill the mighty Dr. Serizawa here."

Daisuke looked slightly offended, but remained silent as they entered Nerv and began to make their way to Central Dogma.

"I assume you're here to fight Ghidorah?" Makoto stated.

"Ghidorah?" Rei questioned.

"Oh, that's what Daisuke decided we should call it," Miki said. "Ghidorah. It means The-One-Who-Is-Many is some indigenous tribe's language."

"Ghidorah," Shinji mumbled. "Sounds familiar to me. Like I heard it in a dream or something."

"Either way," Makoto said as they neared Central Dogma. "We need to get you and Rei to your Entry Plugs. Since we have basically no staff right now to operate the helicopters, Rei's going to have to manually insert you into Godzilla, Shinji."

"Manually?" Shinji asked worriedly.

"Yeah, manually. She'll carry your Entry Plug in her Eva's hands over to Godzilla and stuff it in herself. Fortunately, it's currently lying facedown on the ground, so we won't have to worry about her reaching it. We'll just have to hope that none of the monsters stop her."

"Right," Shinji said as he glanced at Rei. "The monsters are what we need to worry about, not Ghidorah."

"Well, him too," Daisuke said as they entered Central Dogma. "Hopefully, he's too busy with generating that superstorm of his to notice what you're up to, Rei."

They entered Central Dogma and immediately noticed Ryoji sitting unconscious against one of the desks with a pool of blood surrounding him. Sitting in one of his hands was a transmitter.

"Fuck!" Makoto cursed. Miki surged forward and dropped to her knees, examining his wound. "He's been shot, not too long ago either, at most a couple of hours. He's suffering from major blood loss. Shit, he'll need a transfusion."

Daisuke groaned in exasperation. "Shinji, Rei get to your Entry Plugs immediately, no time for Plug Suits. We'll get everything booted up here, and maybe even take care of Ryoji."

Shinji and Rei stood nervously, not sure what to do.

Daisuke rolled his eyes. "Go! We don't have all night!"

With a nod, Rei set down Mari's carrier. "Watch over her. Please."

Daisuke waved his hand at the two teens. "Yeah, yeah, OK. Get moving, damn it!"

* * *

Shinji watched as Rei climbed into her Entry Plug. He shifted nervously from one foot to the other, knowing he should get moving to his own, but something held him back.

"Hey, Rei…."

"Yes?" Rei turned around and gave Shinji from inside her Plug, her hand on the interior sealing button.

"I, well…."

Rei leaned back out and grabbed the front of Shinji's shirt. He gasped as she pulled him into a short, fierce kiss that shocked him. In the span of a few seconds, it communicated everything to him. It was desperate, sensual, and most of all, filled with the kind of innocent love that only teens could have. With a pop, they parted, and she shoved him away. Her expression was filled with a mixture of fear, worry, and hope.

"Go," she said softly.

Shinji nodded silently as he turned and ran off, hoping that somehow, things would turn out OK.

**Notes for the Chapter:**

> I'll admit, I'm not too hot on this chapter, but maybe that's just me.
> 
> Either way, next chapter we finally get to Godzilla/Eva-01 vs. Ghidorah! I hope I'll be able to do it justice, especially as we near the end of the 2nd Part of Evangelion X Godzilla. Chapters 10 and 11 will cover the showdown itself, while Chapter 12 will deal with the aftermath and wrap up Sin From Genesis and set up the 3rd Part of the story.
> 
> Thanks to those who checked out my Attack on Titan story, I really appreciate you guys!
> 
> Until next time!
> 
> -AlphaBeta17 (5/1/20)


	10. Clash of the Gods

**January 1st, 2016**

Ryoji's eyes shot open. He let out a gasp as pain knifed through his body.

"Misato!" He yelled. A flurry of motion suddenly descended on him, and he blindly thrashed at it. Weak and uncoordinated, still crippled from the gunshot wound to his shoulder, a pair of hands was easily able to grab his flailing arms and restrain him.

"Hey, it's just me! It's Makoto!"

"Oh," Ryoji said as his vision came into focus. He was still sitting against one of the desks in Central Dogma, and nearby, Daisuke and Miki were seated at their own monitors, furiously tapping away at keyboards. First aid supplies lay scattered on the ground nearby, and his shoulder was bandaged. "What's going on," he asked wearily.

Makoto stood and gave Ryoji a tired look. "We're deploying Shinji and Rei to try to fight Ghidorah."

Ryoji stared at Makoto blankly. "They don't stand a chance. You know that right?"

Makoto sighed. "Honestly? You're probably right. But it's better than not doing anything. What I'm really interested in is why we found you here with a bullet in your shoulder."

Ryoji managed to clamber to his feet and clutched at his bandaged shoulder carefully. "Thanks, by the way. I'm assuming you gave me a blood transfusion?"

"Yeah, you're fortunate we still had your records on file. Otherwise, we'd have had to shoot in the dark for your blood type. You didn't answer my question, however."

Ryoji rolled his eyes. "I broke in here with Ritsuko, Gendo, and Asuka. We came across Misato, and after I tried to convince my comrades _not_ to kill her, Gendo shot me, and left me to die."

"Wait, Misato was here?" Makoto asked, suddenly apprehensive.

"Yeah, I think Gendo took her and Asuka down to Terminal Dogma, along with Ritsuko at his side."

Makoto turned towards the elevator with an air of determination. "How do I get down there?"

Ryoji's eyes widened. After a moment, his face broke out into a weak grin. "You sure you want to do this? I can get you down there, but you do this, you'll be exposed to my world."

"I don't care," Makoto said firmly. "I can deal with seeing whatever you bastards were up to. We need to free those two down there."

"Oh no," Ryoji laughed. "You don't understand. My world is completely different from Gendo and Ritsuko's. I was never really on their side, you see. I helped them, sure, but it was all in conjunction with the goals of the organization I am truly loyal to."

"What organization?" Makoto asked nervously.

Ryoji smirked. "You'll see."

* * *

Rei's Eva held Shinji's Entry Plug carefully in its left hand as it prepared to make a dash for Godzilla. The running speed of the Eva meant it would only take about 20 seconds, but she would have to avoid Anguirus, Baragon, and Varan, which were all rampaging in Tokyo-3.

Overhead, Ghidorah's storm swirled violently, and thunder and lightning split the sky with blasts of light and sound. Rain poured in a deluge that masked visibility, and wind swept across the destroyed city, spreading the smell of death and destruction.

Rei shivered, even though she was surrounded by LCL. She shifted her Eva's grip on her Prog Katana in its right hand, prepared to use it to defend both herself and Shinji.

"Shinji, Rei, ready to make a dash for it?" It was Daisuke's voice. With Ryoji and Makoto descending beneath Nerv, he and Miki were all that was left to guide Rei and Shinji.

"I'm ready," Rei said firmly.

"Ready as I'll ever be," Shinji said worriedly.

"Alright. Go! Now!" Daisuke yelled.

With a powerful leap, Rei broke her Eva into a sprint, beelining straight for Godzilla. From the corner of her peripheral vision, through the rain and wind, she saw a blur of red bearing down on her. Baragon.

In a fluid motion, Rei pivoted her Eva off its right foot and spun in a circle, swinging her Prog Katana around and catching Baragon across the face right as it jumped at her. With a cry of pain, Baragon went down and Rei continued with her motion into another burst of speed, quickly closing the last few massive strides to Godzilla's side. Sliding to a stop, Rei quickly, but carefully, slid Shinji's Entry Plug into its slot on the back of Godzilla's neck. With a mechanical click, the Plug took hold and was pulled into the mass of flesh of metal.

Rei turned her Eva and adopted a defensive stance, holding her katana with both hands, ready to defend Shinji while he synced with Godzilla. Both Anguirus and Varan were closing in, having been drawn by Baragon's cry of pain. Rei readied herself to take on both monsters at once.

A shadow suddenly obscured her vision, and the pattering of rain on the Eva's metal exterior ceased. Before Rei knew what was happened, she was in the air, moving away from Godzilla.

Rei looked up and froze at the sight. Her Eva was held in Ghidorah's clutches.

Rei swung her katana in a panic, which sliced across Ghidorah's feet, drawing a roar of anger from the golden dragon, which immediately dropped her. Landing spryly, she turned the Eva and prepared to dash back to Shinji. With a jolt of horror, she saw Anguirus and Varan bearing down on a defenseless Godzilla.

Before Rei could move, a bolt of light struck the ground in front of her, blasting her off of her feet. Rolling away to safety, Rei was barely able to raise her katana in time to block another bolt of light.

Ghidorah's gravity beam ricocheted off Rei's katana and smashed into the ground nearby, exploding in a burst of gravitational energy.

Ghidorah landed in front of Rei and reared all three of its heads as it roared into the stormy night. Towering over her Eva, it felt confident in its ability to win this fight. It had been caught off guard by the sharpness of its sword, but the small wound on its feet had already healed.

Ghidorah had fought countless adversaries, and this small mechanical monstrosity would not be the one to defeat him.

Rei backflipped out of the way as Ghidorah lunged with his center head and swung her katana again, this time slashing across Ghidorah's eyes.

As the dragon roared in agony, Rei dove underneath it and attacked its underbelly, swinging her sword back and forth, leaving long streaks of red that stood out against the golden scales.

With one massive flap of his wings, Ghidorah rose up into the air. Peering down his two other sets of eyes while the third healed, he allowed himself to fall back to the ground, intending to crush the Eva beneath his weight.

Rei jumped out of the way just in time and began a flurried dance, weaving in and out of Ghidorah's grasp, slashing at anything she could.

Despite her skill, Ghidorah's healing powers were too effective. Any hit she managed to land would be healed within seconds, and Ghidorah was only getting angrier, not showing any signs of tiredness. Rei, meanwhile, was feeling the burn in her body from the extensive acrobatics she was performing with the Eva, and her movements began to slow.

Growing frustrated, Ghidorah jumped into the air once more, but this time, he fired his gravity beams from all three of his heads, each forming the point of a triangle surrounding the Eva. Drawing the three beams together, Rei's Eva was caught, and floated in midair while he landed in front of her.

Extinguishing all but one of his beams, Ghidorah cackled with his other two heads. Time to end this.

Grabbing hold of the Eva's head and legs with his other two heads, Ghidorah released the gravity beam and prepared to eviscerate it with his center head. Leering over it, he barred his teeth in anticipation of the killing blow.

A blast of radioactive energy came out of the night and impacted on Ghidorah's flank, stunning him with its explosive power. He released the Eva, which quickly scrambled away to safety. Turning in anger, he reared his heads up in surprise.

It was Godzilla, standing with wispy smoke coming from the corners of its mouth. On either side of it lay Anguirus and Varan, both looking worse for wear, but not dead.

Godzilla roared in challenge, and Ghidorah roared back. This was what he was looking forward to. A challenge.

Godzilla burst into a run, its powerful, slender Evangelion legs punching the ground as it rapidly approached Ghidorah, who spread his wings and prepared to meet the challenger head-on.

With a sonic boom that echoed across Tokyo-3, Godzilla collided with Ghidorah.

* * *

The elevator slid open, revealing a dark hallway lit by a single lightbulb. Makoto glanced at Ryoji, who lay wearily on the floor of the elevator.

"We're here, c'mon," Makoto said hurriedly. "We don't have much time."

Ryoji groaned as he sat up and slowly got to his feet. "Hey. Chill. I was shot just a few hours ago, I need to take things slowly."

Makoto stopped at the heavy-looking door with a passcode panel on it. He had no idea how Ryoji planned on getting past it, but he said he had a way to do it.

Ryoji stumbled over to it and pressed his body against the wall next to the door. Reaching into his pocket, he pulled out a transmitter and turned it on.

"Kaji here. Any word on cracking this passcode?"

The transmitter crackled, and a voice came out of it. "Hold the transmitter up the panel, it'll take us a few moments."

Makoto watched in confusion as Ryoji obediently held the transmitter up to the panel.

"What are you doing?" Makoto asked worriedly. "Please tell me you actually know how to bypass the security code."

"I'm not trying to," Ryoji answered. "You don't need to bypass the code if you enter it correctly."

"But how do you know the code!?" Makoto said incredulously.

"I don't. I will in a moment, however."

The transmitter buzzed. "1-0-4-9-5. That's the code."

"Thanks," Ryoji said as he punched in the code. With a buzz, the door slid open.

Makoto stared at Ryoji in shock. "How did…."

"I'll tell you later. C'mon," Ryoji said with a smirk. Makoto rolled his eyes and followed Ryoji into Terminal Dogma.

* * *

Smashing into Ghidorah, Godzilla roared as the three-headed dragon was sent stumbling back from the impact. Not stopping, Godzilla lunged forward with an open mouth and fired a blast of atomic breath directly into Ghidorah's chest, exploding with radioactive energy on impact.

Reaching out with its humanoid Evangelion hands, Godzilla grabbed hold of Ghidorah's right and left heads, slamming them together with a loud crack.

Inside the Entry Plug, the Eva's voice bounced around while Shinji attempted to keep a handle on his sanity. He knew that he stood no chance in combat, so immediately upon syncing, he had relinquished control over to the Eva, not even attempting to fight it.

If any situation called for the full power of Godzilla and Eva-01, this was it.

Ghidorah used its head to hook underneath Godzilla's body and flipped upwards, sending Godzilla flying into the air. Ghidorah quickly released a blast of his gravity beams which connected with Godzilla and sent it smashing into the ground. Lunging forward, Ghidorah slammed down on Godzilla with his full weight.

As Godzilla roared in pain, it grabbed onto Ghidorah's legs and pushed upward, allowing Godzilla to clamber to its feet. It sent Ghidorah tumbling over backward and rushed forward, pummeling the dragon with its fists.

Ghidorah slammed its wings together, stunning Godzilla temporarily as Ghidorah righted itself and surged forward for another attack, landing blow after blow with its heads on Godzilla, who unleashed another blast of atomic breath.

Ghidorah quickly bit down onto Godzilla's head and aimed its breath towards the ground below, where it impacted with an explosion that knocked both monsters backward. Godzilla tumbled heavily to the ground while Ghidorah took the opportunity to fire its gravity beams again, this time connecting and allowing it to lift the monster into the air. Ghidorah cackled at the sight of the helpless monster, and prepared to rip it apart.

A war cry startled Ghidorah, and he turned just in time to see Rei's Eva come running in from the side. Its mouth barred in a guttural roar, it swung its Prog Katana, slicing clean through Ghidorah's right head. The head tumbled lifelessly to the ground as Ghidorah roared and turned on the Eva, landing a heavy blow with its left head which sent the Eva flying backward. Ghidorah jumped into the air and began hovering in place while it allowed time for the head to regenerate from the stump on its neck.

Godzilla was able to get to its feet and took advantage of Ghidorah's state, jumping up and grabbing hold of it around its necks, dragging both monsters down to the ground. As Godzilla wrestled with Ghidorah, Rei jumped onto Ghidorah's back and slashed through the base of its wings, sending both falling to the ground.

Ghidorah could scarcely believe it. This was absolutely unacceptable!

* * *

Makoto ignored the floating Rei clones as he pressed deeper into Terminal Dogma with Ryoji close behind him. They were both carrying pistols that they had found lying on a table near the entrance. Clearly, Ritsuko hadn't expected anyone to be able to enter her lab of horrors.

Deep rumbles kept coming from above, indicating that by now, Godzilla and Ghidorah were likely locked in combat. Makoto hoped that things were going better than he was anticipating.

He froze when he heard a voice nearby. Ryoji motioned down a specific hallway, and Makoto followed.

"….they're probably fighting right now."

"Yes, I imagine so."

Taking a deep breath, Makoto peered around the corner. It was Gendo and Ritsuko who were both sitting at computer monitors, apparently watching events unfold back up at the surface.

He glanced back at Ryoji who nodded. Ryoji's shoulder meant that he was in no condition to fire a gun, so it was up to Makoto.

He swung around the corner and fired his gun several times.

Ritsuko yelled as one of the bullets caught her in the stomach, and she went down. Gendo, who hadn't left his weapon behind, immediately pulled his gun and fired back several times, forcing Makoto to duck back behind the corner.

"I got Ritsuko!"

By the time Makoto glanced back around the corner, Gendo had fled down another hallway. Walking out into the open, Makoto kept his gun trained on Ritsuko.

"Where are Misato and Asuka," he growled as menacingly as he could.

Ritsuko didn't even look at him as she began to cough up blood. "He….he left me. He left me," she gasped.

Makoto sighed as he started towards her. "Listen, you're bleeding. If you want to live, you'll-"

"No. Stay back!" She yelled. "Just let me die in peace."

Makoto stared at her for a second before nodding slightly. "First, tell me where Misato and Asuka are."

Ritsuko groaned in pain as another wave of bloody coughing wracked her body. "They're in a supply closet back the way you came."

After a moment of hesitation, Makoto nodded. "Farewell," he said softly. As he left with Ryoji to go free Asuka and Misato, Ritsuko lay on the floor and closed her eyes for the final time.

* * *

As Ghidorah's wings began to regenerate, Godzilla entered a frenzied state, overcome with raw bloodlust. Ripping and tearing with terrifying speed, it disemboweled Ghidorah again and again, driving itself to madness with fury as the golden dragon continuously regenerated, none of the damage it was receiving having a permanent effect.

Ghidorah groaned in annoyance as Rei sliced off one of his wings again. It had been painful the first time, but now, it was just irritating. This whole battle just wasn't nearly as much fun as he'd been hoping.

With a snort, he decided to end it. The being-that-was-two-beings and the small mechanical being needed to be put in their places.

Ghidorah began to gather energy inside of himself and focused it into his wings. If he was to pull this off, he'd have to time it just right.

Rei was the one to notice the sudden change in the air. "Shinji!" She yelled desperately, hoping he could still somehow hear her.

No response came.

With a concussive blast, Ghidorah released the energy in his wings. Raw gravitational power ripped through Tokyo-3 and destroyed what few structures were left standing. Both Godzilla and Eva-00 were blasted backward and lost in the whirlwind of debris. Nerv itself was flattened, the giant steel pyramid finally caving under the power of Ghidorah.

Ghidorah spread his wings and roared in triumph. He called lightning down from the sky which struck the tips of his wings and spread throughout his body, creating a haunting, ethereal final image of destruction. It was time to end this planet once and for all.

From within the destroyed ruins of Nerv, Miki Saegusa and Daisuke Serizawa sat solemnly underneath several hundred feet of flattened steel. Mari trilled in fear from within her cat carrier next to them, not understanding what had just happened.

Asuka Soryu, Misato Katsuragi, Ryoji Kaji, and Makoto Hyuga looked up at the ceiling of Terminal Dogma and waited with dread for the end. The elevator wasn't responding, and the feeds from the surface had suddenly gone dead. They knew it was coming. It was only a matter of minutes.

Ritsuko Akagi lay dead, deep in the depths of Terminal Dogma, her story already at an end.

Gendo Ikari, having made it to the elevator and escaped back to the surface, moved silently in the lower levels of Nerv. He passed the empty chamber that Eva-01 used to be stored in and stopped briefly. He stared out across the empty space with an unreadable expression.

Rei Ayanami lay trapped within her Eva. She tried to force it to stand, but it now lay crushed underneath rubble that was once the buildings of Tokyo-3. Already exhausted from the battle, the organic mech was unable to move.

Shinji Ikari opened his eyes. This was it. He had failed. The world was ending.

Ghidorah had won.

**Notes for the Chapter:**

> While writing the fight with Ghidorah (and just in general these past few chapters) I tried to employ his gravity powers in interesting ways, as I always felt they were never really used to their full extent in the movies.
> 
> Until next time!
> 
> -AlphaBeta17 (5/10/20)


	11. Third Impact

**January 1st, 2016**

SHINJI

Shinji sighed as the voice of the Eva rang in his head.

_Go away. It's over. You failed, and it's my fault for handing control over to you._

THERE IS ANOTHER WAY TO WIN

_No, there isn't. Just accept it. We're already dead._

SHINJI

I AM YOUR MOTHER

Shinji felt his heart freeze. A cold wave of horror swept through him.

_No, you're lying. That's not possible. My father was lying when he told me that. I didn't believe him. I can't believe him._

IT'S TRUE

I AM YOUR MOTHER

I AM YUI IKARI

Shinji tried to take deep breaths to calm his panicking mind as the horrible truth hit him.

_No. Please, no. This can't be real, this can't be real, this can't be real._

Shinji began shaking as he grabbed onto his head, trying to stop the spinning of a world turned upside down. Pain spiked through his heart, and he gasped for air desperately as he began sobbing. It felt like he was tortured by an unmerciful god. He just wanted it all to end.

_Please, stop. Make it stop, make it stop! I can't take this anymore!_

Shinji felt himself collapse under the immense pressure of the world. He was trapped in his Entry Plug, inside of the monstrous fusion of Godzilla and Eva-01, crushed underneath the weight of Tokyo-3.

There was no escape. His mother was alive, and she was the soul of Evangelion Unit-01.

Shinji screamed as he lost his fragile grip on reality.

* * *

Godzilla burst free from underneath the flattened rubble of Tokyo-3 and came face-to-face with Ghidorah, who was hovering in midair as it prepared to shatter the planet. This was always the most enjoyable part of his never-ending quest to destroy planets. The screams of entire races, entire worlds being violently obliterated in a wave of heat and destruction, their history and collective memory being lost forever...

Nothing could compare to that power. Nothing. And nothing had ever stopped it. So it was with great surprise that Ghidorah glanced down at Godzilla as it emerged from the rubble, the mixture of metal and stone twisting and ripping like paper as the beast clawed its way out. How was it breaking through the layers of solid, compacted rubble? No matter, Ghidorah decided. A momentary setback, no doubt.

Letting out a roar, Godzilla suddenly accessed its Eva powers and began to draw power from the planet itself. The essence of life, and the energy that all matter contained therein, was suddenly accessed and reconditioned to serve the will of one, ultimate being. Every living thing felt it, and for a moment, all life was connected as a single almighty entity. Under the control of Evangelion Unit-01, fused with Godzilla, and housing the shattered spirit of a young boy named Shinji, the world stared death in the eye and snarled a challenge. Today would not be the day of the apocalypse.

Today would mark the beginning of a new world.

The worldwide storm that Ghidorah had generated began to dissipate, atoms of hydrogen and oxygen disconnecting, and the explosive force that was thus released flowing in a wave of pure energy to a single focal point in the ruins of Tokyo-3. Time began to slow as reality shifted, being wrested from its prison beneath the laws of physics by a being like no other, who took the energy and prepared to harness it.

The Sin From Genesis would have its way with the world. Forcing, beating the domain of humanity into submission, this would not be a peaceful, consensual act.

Ghidorah felt a fear he had never felt before grip him. For the first time in his long life, he panicked. Without stopping to calculate his next move, he let out a shriek and opened fire on Godzilla, all three of his gravity beams arching towards it at the speed of light.

This would be a costly mistake on his part.

Godzilla began to levitate as the beams struck it, quickly taking control of the stream of energy and adding it to the energy it was collecting from the planet itself. Glowing both purple and green, the power manifesting itself as visible light, emanating from the creature in a ghostly display of god-like power. Before long, Godzilla rivaled the sun itself in raw luminescence. Despite being the dead of night, it was as bright as day in Tokyo-3.

* * *

Gendo shielded his eyes as he watched the events unfold in the center of Tokyo-3. It had taken a while, but he had managed to climb up and through the wreckage that used to be the giant steel pyramid of Nerv. Now, he stood on the level surface that was Tokyo-3, the ground made of mashed steel and stone. This was all that was left following Ghidorah's assault on the city. Now, something far worse was about to happen.

GENDO

Gendo whirled around, but found himself alone.

"Where are you?" He yelled out. "What are you?"

I AM IN YOUR HEAD

Gendo turned and faced the levitating Godzilla. He couldn't make out anything due to its brightness, but he knew that underneath all the light, lay a fusion of Godzilla and Eva-01.

"Yui? Is that you?" Gendo could hardly believe it. Somehow, his wife was speaking to him, directly into his head.

I AM DISAPPOINTED IN YOU

Gendo froze. "What? What do you mean, disappointed? I did everything we planned. Now, you have ascended. You can defeat Ghidorah, and inhabit Rei's body! We can be together again!"

I WAS WRONG

WE WERE WRONG

"No!" Gendo shouted at Godzilla. "We weren't wrong! Don't say that! Come back to me! Please, I can't be wrong! All of this would have been for nothing!"

I NEVER AGREED TO YOU ABANDONING OUR SON

BUT THAT'S WHAT YOU DID

MUCH LONELINESS AND FEAR RESIDES WITHIN HIM

YOU WILL SUFFER FOR HURTING HIM

YOU

WILL

SUFFER

Gendo began quaking in fear as the uncontrollable wrath of an angry mother washed over him."No! Please, forgive me Yui!" Gend begged, dropping to his knees. "I never wanted to hurt him!"

YOU LIE

I KNOW YOU

I WAS LIKE YOU

I THOUGHT OF MYSELF AS ABOVE OTHERS

JUST AS YOU DO

YOU ABANDONED HIM

A CHILD

WHO HAD JUST LOST HIS MOTHER

"And I had just lost my wife!" Gendo was in a state of hysteria as his entire purpose for existing, bringing back his wife, came to fruition in the most nightmarish way possible. "I was left with a son who could never fill the void you left, so I ran. I ran away, and I didn't look back."

YOU'RE A COWARD

"Yes," Gendo mumbled. "I am. But am I so evil for devoting myself entirely to bringing you back? It worked, didn't it? Here you are."

I DON'T CARE ABOUT RETURNING TO THE MORTAL WORLD

YOU STRUCK MY SON

MADE HIM FEEL ALONE

FORGOTTEN

WORTHLESS

YOU NEVER ACKNOWLEDGED HIS EXISTENCE UNTIL YOU NEEDED HIM

I WAS MISTAKEN TO TRUST YOU WITH HIM

I WAS MISTAKEN ABOUT TAKING AN INNOCENT GIRL AND MOLDING HER IN MY IMAGE

MOST OF ALL

I WAS MISTAKEN ABOUT YOU

"I'm….sorry," Gendo whispered. He bowed his head as he accepted whatever judgment God would bestow upon him.

GOODBYE GENDO

BURN IN HELL

I'LL BE JOINING YOU EVENTUALLY

THEN

WE WILL BE TOGETHER

FOREVER

* * *

For a brief instant, time seemed to a complete halt.

Then, everything was aflame.

What would later be termed the Third Impact was, like the Second Impact, simply an explosive release of destructive energy in a single instant. It breached the upper layers of the atmosphere, where raw, unfiltered energy was released back into the world in a volatile fashion, spreading quickly and violently like a raging typhoon. Temperatures worldwide began to drop, and for the first time in fifteen years, the world felt the sharp bite of coldness.

This concentrated blast of raw energy hit Ghidorah with the force of a dying star. Far surpassing the size of the largest nuclear weapons, its destructive power was only rivaled by the Second Impact, and asteroid impacts that had occurred throughout the millions of years of Earth's prehistory. It would have killed Ghidorah had he not taken one of the most drastic measures he had ever attempted.

At the last second, he hardened his scales to form an impenetrable exterior that was unbreachable by anything, including gods.

The cost was that it would immobilize him for at least several months.

As the flames released by Godzilla's blast swept across his body, Ghidorah realized just how much he had underestimated his opponent. He had treated it like any other, but in actuality, he should have been prepared for anything. This innocent little world wasn't so innocent after all. It had tampered with creation, and in doing so, had created a monster unlike any before it.

How foolish of him. Now, he would have time to reflect, and to prepare for his eventual release from his self-imposed prison.

He would not fail again.

* * *

In the same instant that Godzilla triggered the Third Impact, time ground to a halt as Shinji hid from the being that had sheltered him for the first nine months of his life.

SHINJI

Shinji groaned in pain. His head felt like was being split apart, and he felt tired. So unbelievably tired.

_Leave me alone._

IT'S TIME FOR ME TO EXPLAIN EVERYTHING TO YOU

Shinji felt his gut tighten as anxiety spiked through him.

_No, please don't. I don't want to know._

REI IS ONE OF MANY GIRLS YOUR FATHER AND I ENGINEERED TO BE ME

_No._

SHINJI

REI HAS MY FACE

REI HAS MY BODY

REI WAS TO BE MY VESSEL

Shinji dug his hands into the flesh of his face, tearing and ripping as he tried to kill himself before he could hear any more of this terrible truth. Existence was becoming too painful for him to bear. Nothing, not even those he loved, seemed to be worth the effort to continue onward. He just wanted it to end.

_Go away. I don't want to hear this. Just let me die._

I HELPED CREATE THE EVANGELIONS

_Stop._

ASUKA'S MOTHER IS INSIDE HER EVA AS WELL

RITSUKO'S MOTHER IS INSIDE REI'S EVA

_Please, stop_ , Shinji begged quietly as his tears and blood mixed with the stale LCL.

AND I JUST KILLED YOUR FATHER

_I don't care._

GHIDORAH HAS BEEN CRIPPLED

_I don't care._

I STILL POSSESS SOME LEVEL OF OMNIPOTENCE

I CAN HEAR THE THOUGHTS OF EVERYONE

I BELIEVE THEY ARE ALREADY CALLING WHAT I JUST DID THE THIRD IMPACT

_I don't care!_

YOU SHOULD

I JUST SAVED THE WORLD FROM GHIDORAH

_Maybe you shouldn't have!_ Shinji yelled out with his mind in despair. _Look at what you did! You're a monster! Just like my father!_

DON'T SAY THAT

_Yes! I will say that!_ Shinji yelled. Years of holding his mother on a pedestal came crashing down, and it was breaking him. _You….you say that Rei is a 'vessel' and has your body! How could you?_

I CARED ONLY FOR MYSELF

I'M SORRY

_No! You don't get to be sorry after all that! Not after creating the Evangelions, and tearing into a young girl, forcing her to look like you! You're evil! You and father both!_

I MADE A MISTAKE

_You made a mistake._ Shinji began to chuckle humorlessly as his self-torture reached excruciating levels. His face was unrecognizable as his fingernails tore into his own flesh and spilled his own blood. _You made a mistake? Really? That's what you call what you've done?_

IT WAS NECESSARY

_No! It wasn't! You're a monster! A monster!_

Evangelion Unit-01 snarled at the boy in anger, as a mother's contrite nature gave way to a predator's rage.

DON'T BLAME THIS ONLY ON ME

I WOULDN'T HAVE BEEN ABLE TO DO THIS WITHOUT YOU

THIS IS YOUR DOING

YOU AND I ARE BOTH GUILTY

YOU HEAR ME

WE ARE BOTH GUILTY

Shinji screamed in utter anguish as his mother's angry voice shrieked in his ears.

* * *

Several hours later, roaring in pain as the last of the energy left his body, Godzilla sank back to the scorched earth. His massive feet settled on the compacted ground, which groaned under the monster's immense weight. Godzilla opened his eyes as the sun peaked over the horizon to the east.

Silhouetted against it was Ghidorah. Standing tall with his wings outstretched, the three-headed dragon was a golden statue. Unable to move, it would remain frozen in place for at least several months.

Glaring at Ghidorah, Godzilla exhaled slowly. Internally, a battle was being raged between mother and son, the mother hurling angry abuse at the son, who had lost any semblance of strength he may have once attained.

Godzilla was tired. For the first time in months, he was in complete control of himself. It was like he had awoken from a long, horrible dream. His skin ached where pieces of metal jutted out of him, and his very bones hurt from the force of the blast he had involuntarily expelled.

He hated it. Everything. The world hated him for existing when he had never wanted to exist. Life used to be simple, and easy, but when he was irradiated, he became a monster. He had come to Tokyo-3 in a rage, trying to find the source of a strange call. When he hadn't found it, he had lashed out in anger.

The destruction and death had felt good, especially when he was the most powerful being in the world.

But then….the Evas had shown up. Violent and bloodthirsty in a way he never was, he was forced to change in order to defeat them. Then, he had been assimilated into one. Existence had become lost to him as he spent two months trapped. Motionless. Sharing his body with a raging monster, and a small, scared boy. Now, these two beings were locked in turmoil together, one lost inside the anger of the monster that it had become, and the other cowering in self-hating fear.

Godzilla couldn't bring himself to care. Slowly, he began to move. Placing one huge food in front of another, Godzilla walked slowly away from Tokyo-3. Away from the scorched earth and twisted metal.

In time, both the boy and the monster within him quieted. Godzilla sensed despair and sorrow seeping off the boy. He blamed himself for everything. If Godzilla could comfort the boy, he would have. The monster, on the other hand, he wanted to hate. He wanted to tear himself apart and expel it from his body.

But he no longer cared. He couldn't bring himself to hate it. Existence was unending pain, and fighting it wasn't worth the effort.

As Godzilla made his way away through the countryside of Japan, he took note of his surroundings. Far from Tokyo-3, everything seemed so peaceful. Snow was beginning to fall from the sky. It reminded him of a time long ago, back before he was Godzilla.

If only he could return to such times.

Godzilla sighed. He sank to the ground and wrapped his tail around his misshapen body.

With a pop, he ejected the Entry Plug, which landed on the snow below.

The boy would have to make his own way in the world now.

Godzilla was done fighting.

* * *

It took many hours before Shinji exited the Entry Plug slowly and peered out at the world around him. Dried blood caked his ravaged face, and he reeked of LCL. He was on a mountainside, and it was midday. Godzilla's immense body towered over him, its eyes closed and its breath barely noticeable.

It had given up.

Shinji watched with child-like fascination as his breath appeared in front of his face as a faint vapor. The ground underneath his feet was white, and soft.

Snow. Cold. These were things unfamiliar to Shinji. He knew of their existence, of course, but he had never experienced them before.

The world he knew didn't possess such things.

This new world did.

Taking a deep breath, Shinji began to place one foot in front of the other. Operating only on instinct, he was running away.

A thought came to him, and he stopped.

_Rei._

Her face appeared in his head, only to quickly morph into a twisted, angry snarl. Perhaps that was what his mother looked like. Shinji turned and stared up at Godzilla. Within that monstrous abomination lay the soul of the being who had given birth to him. The same soul who had done such terrible things, he could hardly believe that she had helped create him. But then again, it had created this new world. Maybe only monsters held the power to create.

_Should I go back to Tokyo-3? Try to find Misato, Asuka, and Rei?_

For a brief second, he considered it. Then, he was assaulted by the memory of what had just transpired. Images, feelings of destruction, death, and desolation filled his soul, and he collapsed to the ground.

_I can't do it. I'm not strong enough. I never was, and I never will be. If I try to go back, I'll only make things worse._

A roar came from overhead. Shinji looked up and spotted what looked like a giant pterosaur passing overhead. It glanced down at him and let out a booming squawk before continuing on its way, sailing into the distance.

Irreversibly damaged, and filled with monsters awoken by Ghidorah, this was a new world. And Shinji wasn't going to try to fight it.

_I'm sorry Asuka. I never understood you, and now I never will._

_I'm sorry Misato. I was never strong enough for you._

_I'm sorry Rei._

Shinji felt his breath hitch.

_I'm sorry for everything. You can keep moving forward without me. You're so much stronger than me. I know you can do it. You'll take care of Mari, and defend the world where I couldn't._

Shinji got to his feet and bid a silent farewell to Godzilla. A part of him wanted to hate Godzilla, for coming to Tokyo-3, and dragging him from his miserable, but boring life into an extraordinarily painful, wonderful, and confusing world, filled with both those who hated him, and those who loved him.

But Shinji couldn't hate Godzilla. He no longer cared enough to feel such extreme emotion.

He didn't want to care about anything ever again.

_Goodbye_ , he silently said, before turning around and facing the unknown. He raised a hand to his face, covered in dried blood and long, self-inflicted marks which would surely scar. A permanent reminder of the destruction that had been dealt to the planet, and who was ultimately responsible for allowing it to happen.

With only his thoughts as his companion, Shinji left his old self behind. He walked off into the wilderness, and into his new life.

**Notes for the Chapter:**

> I tried to go a bit philosophical here, and pretty much abandoned the plot along the way. I can't say I'm pleased with it, but it's vitally necessary for Part III of Evangelion X Godzilla to be where it is right now. And I guess it wouldn't be Evangelion if right when reaching the climax, logic and reason (along with the plot) are thrown out the window in favor of a deeply existential examination of character.
> 
> This chapter was really about two things: Gendo's death, and Shinji's death. The antagonist from Part I is gone, and the antagonist from Part II is frozen in stasis. Shinji has given in and is running away, and in doing so, abandons everything he was building towards the entire story. I hope this wasn't disappointing to anyone, but I'll just say for now that the story isn't over.
> 
> Next week will be the final chapter of Sin From Genesis, and will return to the ruins of Tokyo-3. Shinji may have given up, but the other characters haven't.
> 
> -AlphaBeta17 (5/15/20)
> 
> After taking a break from writing for a couple of months, I returned to this story and reread it in its entirety before starting Part III of Evangelion X Godzilla. This particular chapter stuck out to me as both rushed and lacking in dramatic substance. Filled with grammatical errors, and missing some key elements that are important for the overarching story, I decided to retool the chapter a bit. This version here is far superior to the original, and I apologize to readers of the original version for the lack of care I put into it.
> 
> -AlphaBeta17 (9/14/20)


	12. King of the Monsters

**January 9th, 2016**

Rei stared out the window of the helicopter as snowy landscape passed underneath in a white blur. Her face was a mask of coldness that reflected the new world that the Third Impact had created. A world of snow and ice, defined by loss and loneliness.

She thought back to just a few days prior, when she was with Shinji. How peaceful everything had somehow seemed, and how happy she had been.

Now, Shinji was gone. Nobody knew where he was, only that following Third Impact, Godzilla had stumbled away from the flattened ruins of Tokyo-3 and collapsed on a mountainside some 50 miles away. Shinji's Entry Plug was found open on the ground nearby, and it was empty.

The assumption everyone else had was that Shinji had run away for good, but Rei didn't believe it. She _couldn't_ believe it. The Shinji that she knew had grown so much in the short time she had known him. He would never abandon everyone.

He would never abandon her.

* * *

**One Week Earlier**

Rei slowly opened her eyes, and squinted against the bright sunlight. She tried to think back to the last thing she remembered, and her head began to hurt. What had happened?

"Ah, you're awake," someone said.

Rei's vision was suddenly blocked by someone. "Who are you?" She managed to ask. Her vision slowly came into focus, and her eyes widened in surprise.

"Fuyutsuki?"

Fuyutsuki smiled gently at her. "I'm glad to see you're still in one piece. We weren't sure you would still be alive when we dug your Eva out of the ground."

Rei slowly sat up and rubbed her forehead. "Out of the ground?" She was lying on the ground next to her Entry Plug, and her Eva sat slouched over some distance away, next to a large pile of debris-filled dirt, and a large hole. Three people were gathered around her, and she knew all of them. "Maya? Shigeru? What are you guys doing here?"

"Ah yes, I should probably explain what happened after your Eva was buried," Fuyutsuki said carefully. He stood and gestured towards what was once Tokyo-3.

The ground was made of a mix of metal, stone, and dirt, all mashed together to create a solid, flat surface that stretched for miles. Easily visible was Ghidorah, who stood tall and proud in the distance, seemingly frozen in place. Also visible was-

"What's that?" Rei asked in shock, her eyes widening.

Sitting just a short distance away from her was a giant monster. It was covered in brown, downy fur, and had a face that looked vaguely like a cross between a dog and a lion. It stared down at her and cocked its head curiously.

"Oh don't worry about him," Fuyutsuki said with a grin. "This is King Caesar. He's the reason you're free. He dug your Eva out from the ground, and we were able to coordinate with Maya and Shigeru to free you from your Entry Plug."

Rei glanced at the two former Nerv technicians and nodded slightly. "Thank you."

"We joined with an ancient organization following our departures from Nerv," Fuyutsuki continued. "The Followers of Caesar. We'll explain more once we're in the air."

"But what about Shinji?" Rei asked softly.

Fuyutsuki's expression changed. "There's a lot we have to fill you in on."

* * *

Rei sat silently while she digested everything Fuyutsuki had told her on the helicopter ride out of Tokyo-3. Daisuke (who now had an eye patch), Miki, Shigeru, Maya, Fuyutsuki, Ryoji, Misato, and an unusually silent Asuka all watched Rei carefully. They all knew that she probably wouldn't take well to the news about Shinji, it was just a matter as to how she would react.

"So he's gone?" Rei's tone was filled with disbelief.

"Yes, unfortunately," Misato said. "The Followers of Caesar tracked Godzilla some 50 miles away from Tokyo-3, and found Shinji's Entry Plug abandoned next to it. The snow completely covered his tracks. He could be anywhere by now."

Rei shook her head. "I want to see it."

Fuyutsuki sighed. "It'll take us a few days, but we can arrange that."

Rei looked up at him. "I also want to know what the Followers of Caesar are."

Ryoji stepped forward. His arm was in a sling, and he looked exhausted. "Fair enough. I joined them several years ago, after being shown the slumbering King Caesar in an underground cavern. He's been that way for thousands of years, and has never stirred once. Until Ghidorah woke every single monster worldwide."

"But why were you working with Nerv?"

Ryoji sighed. "I was a spy. It wasn't easy, pretending to agree with Gendo's plans, but if King Caesar was to be woken up, I had to let Gendo set everything in motion. I apologize for any pain I've caused you as a member of Nerv, and as someone who was in the know about Gendo's schemes."

"And you're sure Gendo is dead." Rei's statement was filled with an edge of fear.

Makoto nodded. "No one could have survived the blast that Godzilla released. The governments of the world have already termed it the Third Impact, and it could be even more devastating than the Second Impact was, in the long run."

"The Third Impact reversed the effects of the Second Impact to the extreme," Shigeru said. "The world is now on the verge of another ice age. Agriculture will suffer tremendously as a result, which could lead to the death of billions."

"But that's not our biggest problem," Misato interjected. She glanced at Ryoji, and he nodded. She took a deep breath before continuing. "Ghidorah. He's in a frozen state right now, but we're almost certain that he'll unfreeze within a few months. We have until then to figure out how to defeat him, especially with Godzilla out of the picture, since only Shinji can control it."

Rei shuddered at the thought of Godzilla. She now knew her origins, and the thought of Shinji's mother being the soul of the Eva that had fused with Godzilla frightened her more than Ghidorah ever could. Her true mother had been killed, and her body was molded to be a copy of Yui Ikari's. The only way Rei was still functioning was by doing what she was best at. Putting on a mask and filling herself with a void of emptiness. Emotion would only bring pain.

"We do have a few ideas," Fuyutsuki said with an air of optimism. "King Caesar, for one. He's remarkably intelligent, and dedicated to protecting all life on Earth. Since Ghidorah wants to destroy all life, King Caesar stands in opposition to him."

"He's is able to understand basic human language," Ryoji cut in, "and he's been helping us however he can. When we found out that you were trapped in your Eva underground, he didn't hesitate to dig you out. He also dug up Asuka's Eva, as well as all of us that were trapped at Nerv. We all owe him our lives."

Miki nodded knowingly. "Without him, we would have all perished eventually."

Ryoji nodded in agreement. "There is something else. Back before Godzilla attacked Tokyo-3 for the second time, Nerv uncovered ancient documents on an island in the south Pacific, Infant Island. I managed to steal these documents in the chaos that followed, and the Followers of Caesar were able to translate it. It speaks of a King of the Monsters. It says that this King will be able to rally monsters together to defeat an otherworldly threat. We believe that King Caesar is this monster, and that he will lead other monsters into battle against Ghidorah."

"Or it could mean Godzilla," Rei said quietly. "If the King of the Monsters is Godzilla, then we need to devote whatever resources the Followers of Caesar have to finding Shinji."

Misato exchanged looks with Ryoji and she sighed. "Rei, I don't think Shinji wants to be found. He ran away, remember?"

"He probably had a good reason," Rei insisted. "I believe in him. Why won't you?"

"Forget Shinji!" Asuka suddenly snapped. Everyone turned to her, and she glared at them all.

"We don't need him. He abandoned us all, right when we needed him most! We can do this without him."

"No," Rei said firmly. Asuka turned her glare on Rei, but she wasn't about to back down. "We need to find Shinji."

Asuka looked like she wanted to start yelling at Rei, but her angry expression slowly dissolved into a more subdued, bitter one. "Fine. Keep believing in him. But I'm warning you, you're setting yourself up for disappointment. He doesn't want any part of this. It's up to us now. I don't know about you, but I'm going to keep fighting." Asuka turned to Fuyutsuki and set her jaw. "I'll do whatever I can to help."

He nodded in thanks, then turned to Rei. "And you? Will you help us?"

Rei looked like she wanted to say something more, but her expression lowered, and she nodded slowly. "I'll help you. But please, let me go to Godzilla. Maybe I'll find something that your people can't."

Fuyutsuki gave her a sad smile. "OK. But don't get your hopes up too high. We don't want to see you get hurt." With that, he turned back to everyone.

"We have each other, and the full resources of the Followers of Caesar. There aren't a lot of us, but with King Caesar, and Rei and Asuka's Evas, maybe, just maybe, we stand a chance in this new world."

* * *

Rei's feet crunched in the powdery snow as she approached the empty Entry Plug. Her feelings were in an uproar, as every step brought her closer to the realization that what Asuka had said was true.

Shinji had run away. He had abandoned her.

She stopped in front of the Entry Plug and turned to stare up at Godzilla. It didn't even seem like he was breathing. Staring at his grotesque figure, she couldn't help but feel sorry for him. Even though he had caused her so much pain, now, in such a vulnerable state, she couldn't feel any anger at him. He was just an animal, and he didn't deserve what had happened to him.

With a deep breath, she stepped into the Entry Plug.

Her breath came in frosty breaths that disappeared into the dark interior of the Plug. She peered around the inside of it, looking for any clue to Shinji's whereabouts.

She couldn't find any.

Mildly frustrated, she stepped back out into the open. She looked towards the helicopter in the distance, where a pilot whose name she didn't know, who was loyal to a group of people who worshipped an ancient god, waited impatiently for her to come back. As an Eva pilot, her services were needed more than ever. In the week since she was rescued from the remains of Tokyo-3, the monsters that now roamed worldwide had begun attacking various cities again. This time, however, they were doing it independently of each other. There was no coordination, or underlying cause behind the attacks. The attacks were happening, and they needed to be dealt with. People needed to be protected, and King Caesar couldn't do it by himself. As a result, both she and Asuka had been sent all over the world to battle monsters.

Already, Rei had battled several. While the fights themselves weren't difficult, at least compared to previous battles she had fought, the constant onslaught was growing exhausting. With no real home, she was getting very little sleep, catching what little rest she could on helicopter rides around the world, accompanying her Eva.

At least Ritsuko's meddling with Orga's DNA was proving to be useful in regenerating the Eva after each battle. Rei almost wished Ritsuko was still alive, so she could confront the evil scientist for what she had done to her, and to her mother.

Moyoko Ayanami. Rei wondered what her mother had been like. She would never know, thanks to the crimes of Gendo, Ritsuko….and Yui Ikari.

Rei reached up to feel her own face. Yui's face.

Staring at Godzilla, Rei felt a sense of revulsion overcome her. Not for Godzilla, but for the monster that had forcibly merged with Godzilla. It was almost impossible to believe that within that giant mess lay Shinji's mother, who was just as monstrous as Gendo, if not more so.

Rei shook her head. Shinji's mother, the monster. How could both parents of such a sweet boy be so cruel?

Then there was Shinji himself. He was gone, with no clue to where he now was. The only trace left of him was Mari. Miki had kept her safe during everything with Ghidorah, and following her rescue, she had returned the one-eyed black cat to Rei.

Rei turned to stare off into the distance. Somewhere out there was Shinji. A part of her wanted to forget everything and just go look for him, but seeing his empty Entry Plug firsthand was eye-opening.

He was gone. And he wasn't coming back.

Rei started walking back towards the helicopter. It was time to forget the Ikari family. All three of them had impacted her in significant ways, and she would carry a part of each of them with her at all times.

Yui, whose face Rei now wore.

Gendo, who had raised her to be cold and lifeless.

Shinji, who had brought out her true self.

_Goodbye, Shinji. I hope wherever you are, you are happy._

**Notes for the Chapter:**

> And that concludes Sin From Genesis. Compared to the ending of A God Incarnate, this is certainly much more somber and downbeat. I don't feel the same sense of accomplishment I did finishing that one. Maybe that's just because of where my head is right now.
> 
> It was always planned for things to turn out this way, but the real-life stuff going on the world right now has certainly impacted my headspace, and Evangelion being, well, Evangelion, meant it simply wasn't very fun to write about, what with everything going to shit in the real world, and I think unfortunately the writing suffered for it.
> 
> Ah, I should just stop. I've said similar stuff in my past several author's notes. I guess I'll just say that if these last few chapters were disappointing, then I do apologize for that. I appreciate everyone who has stuck with this story up to this point, I really do. This is my first fanfiction, and to be honest, at times it feels like I bit off more than I can chew. At this point, I'm 2/3rds of the way done, and everything is mapped out to the end, so I'm going to keep trucking through it. I am excited for what's planned, and I hope you all will enjoy it as well.
> 
> The first chapter of Evangelion X Godzilla Part III: King of the Monsters will be up next Friday night, as well as a 13th bonus chapter, where I'll list all the references to Godzilla monsters and lore I put into the story, and well as the soundtrack that I assembled to help me write, same as I did for A God Incarnate.
> 
> Until then, thanks for reading!
> 
> -AlphaBeta17 (5/22/20)


	13. Soundtrack and Notes

**Notes for the Chapter:**

> As with A God Incarnate, this final chapter is not a part of the story. It is divided into two parts: a list of the various songs I listened to (all composed by Shiro Sagisu) to help me write and visualize scenes, and various references to pieces of Godzilla lore I adapted for the story.
> 
> The songs come from seven sources: the second and third soundtrack albums for the original TV show, the original soundtracks for the three currently released Rebuild movies, the soundtrack from Shin Godzilla, and the soundtrack from The End of Evangelion.
> 
> If you aren't interested in any of that, skip to the end of the chapter where I have an announcement to make.

**Chapter 1 - Ghidorah**

-God's Message (From Evangelion: 3.0 You Can (Not) Redo)

-Scarred and Battled (From Evangelion: 3.0 You Can (Not) Redo)

**Chapter 2 - Awakening**

-The Day Tokyo-3 Stood Still (From Neon Genesis Evangelion II)

-In the Depths of Human Hearts (From Neon Genesis Evangelion III)

-Godzilla Restarts (From Shin Godzilla)

**Chapter 3 - Biollante**

-Lucifer's Cry (From Evangelion: 1.0 You Are (Not) Alone)

-Under a Burning Sky (From Shin Godzilla)

-Cruel Dilemme III (From Evangelion: 1.0 You Are (Not) Alone)

**Chapter 4 - Return to Reality**

-Instabilite Orchestre (From Evangelion: 2.0 You Can (Not) Advance)

-Robe des Champs (From Evangelion: 2.0 You Can (Not) Advance)

-Crime of Innocence (From Neon Genesis Evangelion III)

**Chapter 5 - Descent into Madness**

-Strategie "Yashima" (From Evangelion: 1.0 You Are (Not) Alone)

-Normal Blood (From Neon Genesis Evangelion III)

-Those Women Longed For the Touch of Others' Lips, and Thus Invited Their Kisses (From Neon Genesis Evangelion III)

**Chapter 6 - Moonlight**

-A Crystalline Night Sky (From Neon Genesis Evangelion II)

-Tranquillite (From Evangelion: 2.0 You Can (Not) Advance)

**Chapter 7 - Terminal Dogma**

-Interference of Others (From The End of Evangelion)

-The End of Midsummer (From The End of Evangelion)

**Chapter 8 - Ghidorah's Arrival**

-Return to Ash (From Evangelion: 3.0 You Can (Not) Redo)

-L' Apotre de la Lune (orchestre) (From Evangelion: 3.0 You Can (Not) Redo)

**Chapter 9 - The Wrath of Ghidorah**

-Betrayal (From Evangelion: 3.0 You Can (Not) Redo)

-Destiny (From Evangelion: 2.0 You Can (Not) Advance)

**Chapter 10 - Clash of the Gods**

-Out of the Dark (From Evangelion: 3.0 You Can (Not) Redo)

-The Wrath of God in All Its Fury (From Evangelion: 3.0 You Can (Not) Redo)

**Chapter 11 - Third Impact**

-Defeat is No Option (From Shin Godzilla)

-Who Will Know (From Shin Godzilla)

-Famously (From Shin Godzilla)

**Chapter 12 - King of the Monsters**

-L' Apotre de la Lune (2 piano) (From Evangelion: 3.0 You Can (Not) Redo

-Cruel Dilemme IV (From Evangelion: 1.0 You Are (Not) Alone)

* * *

-Planet X (and its native Xilien race) are taken from the 1965 Godzilla film 'Invasion of Astro-Monster', where Ghidorah fought Godzilla and Rodan. The Xiliens would return in the 2004 film 'Godzilla: Final Wars'.

-Desghidorah appeared in the 1996 film 'Rebirth of Mothra'.

-Keizer Ghidorah appeared in 'Godzilla: Finals Wars' as an evolution of Monster X.

-Gigan first appeared in the 1972 film 'Godzilla vs. Gigan' as a pawn of the M Space Hunter Nebula Aliens, and actually fought alongside Ghidorah, whereas here, he battles him to the death.

-Gigan's teleportation ability comes from the Atari/Pipeworks Godzilla video games.

-Miki Saegesu first appeared in the 1989 film 'Godzilla vs. Biollante' and would go on to become the human character with the most appearances in the entire franchise, appearing in six Godzilla films from 1989-1995. In those movies, she was psychic, which I referenced here by having her be an ecological neurologist.

-Daisuke Serizawa appeared in the original 1954 Godzilla film as a scientist who creates the Oxygen Destroyer, the weapon that ends up killing Godzilla. He would go on to be referenced by name with the character Ishiro Serizawa in the Legendary Monsterverse films 'Godzilla' and 'Godzilla: King of the Monsters' from 2014 and 2019 respectively.

-Biollante comes from the film 'Godzilla vs. Biollante' where she was created using plant cells, Godzilla cells, and the soul of a young girl. Obviously, her creation is completely different here.

-Gezora, Ganimes, and Kamoebus all come from the 1970 film 'Space Amoeba' with Kamoebus going on to appear (albeit as a corpse) in the 2003 film 'Godzilla: Tokyo S.O.S.

-The Giant Sea Serpent comes from the 1967 film 'King Kong Escapes' and yes, that is its official name.

-The Giant Octopus (again, that is its official name) first appeared in the 1962 film 'King Kong vs. Godzilla'.

-Kamacuras first appeared in the 1967 film 'Son of Godzilla'.

-Ebirah first appeared in the 1966 Godzilla film 'Ebirah, Horror of the Deep'.

-The pterosaur monster that Shinji sees at the end of Chapter 11 is in fact Rodan, who will appear in full in King of the Monsters.

* * *

**Announcement**

I've decided to delay the first chapter of King of the Monsters to next week, so if anyone was looking forward to that, I apologize. I've been struggling with motivation to write for Evangelion X Godzilla, so after Chapter 1 of King of the Monsters is uploaded next Friday night, I'm going to be dropping the weekly upload schedule in hopes that the finished chapters will be of a higher quality. I won't be dropping my weekly schedule for my Attack on Titan X Godzilla story though, as right now I'm just a lot more motivated to write for it (the fact that a trailer for season 4 of Attack on Titan dropped today, confirming that its release is still on schedule, while Evangelion 3.0+1.0 has been delayed indefinitely, certainly doesn't help matters.) Ultimately, I want to deliver a story to you guys that I can be proud of, and if I force myself to push out chapters, then the quality will suffer.

Thanks again to all of you that have stuck with this story so far, it seriously means a lot to me.

-AlphaBeta17 (5/29/20)


End file.
